1XNR | pdb_00001xnr

Crystal Structure of an Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center

PDB DOI: https://doi.org/10.2210/pdb1XNR/pdb
NAKB: 1XNR

Classification: RIBOSOME
Organism(s): Thermus thermophilus
Mutation(s): No

Deposited: 2004-10-05 Released: 2004-12-14
Deposition Author(s): Murphy, F.V., Ramakrishnan, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.273 (Depositor), 0.256 (DCC)
R-Value Work:
0.227 (Depositor), 0.216 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of a purine-purine wobble base pair in the decoding center of the ribosome.

Murphy, F.V., Ramakrishnan, V.

(2004) Nat Struct Mol Biol 11: 1251-1252

PubMed: 15558050 Search on PubMed
DOI: https://doi.org/10.1038/nsmb866
Primary Citation Related Structures:
1XNQ, 1XNR

PubMed Abstract:
Here we report the crystal structures of I.C and I.A wobble base pairs in the context of the ribosomal decoding center, clearly showing that the I.A base pair is of an I(anti).A(anti) conformation, as predicted by Crick. Additionally, the structures enable the observation of changes in the anticodon to allow purine-purine base pairing, the 'widest' base pair geometry allowed in the wobble position.

Organizational Affiliation

Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

Macromolecule Content

Total Structure Weight: 791.8 kDa
Atom Count: 52,075
Modeled Residue Count: 3,918
Deposited Residue Count: 4,078
Unique protein chains: 20
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S2	D [auth B]	256	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371 Go to UniProtKB: P80371
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80371
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S3	E [auth C]	239	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372 Go to UniProtKB: P80372
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UniProt Group	P80372
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S4	F [auth D]	209	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373 Go to UniProtKB: P80373
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UniProt Group	P80373
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S5	G [auth E]	162	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5 Go to UniProtKB: Q5SHQ5
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHQ5
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S6	H [auth F]	101	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8 Go to UniProtKB: Q5SLP8
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SLP8
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S7	I [auth G]	156	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291 Go to UniProtKB: P17291
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UniProt Group	P17291
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S8	J [auth H]	138	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9 Go to UniProtKB: P0DOY9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY9
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S9	K [auth I]	128	Thermus thermophilus	Mutation(s): 0
UniProt
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80374
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S10	L [auth J]	105	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7 Go to UniProtKB: Q5SHN7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHN7
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S11	M [auth K]	129	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376 Go to UniProtKB: P80376
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80376
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S12	N [auth L]	135	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3 Go to UniProtKB: Q5SHN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHN3
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S13	O [auth M]	126	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377 Go to UniProtKB: P80377
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80377
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S14	P [auth N]	61	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6 Go to UniProtKB: P0DOY6
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UniProt Group	P0DOY6
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S15	Q [auth O]	89	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76 Go to UniProtKB: Q5SJ76
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UniProt Group	Q5SJ76
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S16	R [auth P]	88	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3 Go to UniProtKB: Q5SJH3
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJH3
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S17	S [auth Q]	105	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY7 Go to UniProtKB: P0DOY7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY7
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S18	T [auth R]	88	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0 Go to UniProtKB: Q5SLQ0
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SLQ0
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S19	U [auth S]	93	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2 Go to UniProtKB: Q5SHP2
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UniProt Group	Q5SHP2
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein S20	V [auth T]	106	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380 Go to UniProtKB: P80380
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80380
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
16S Ribosomal protein THX	W [auth V]	27	Thermus thermophilus	Mutation(s): 0
UniProt
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIH3
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
16S Ribosomal RNA	A	1,522	Thermus thermophilus
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Molecule	Chains	Length	Organism
Entity ID: 2
Anticodon tRNA	B [auth X]	11	N/A
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Molecule	Chains	Length	Organism
Entity ID: 3
mRNA	C [auth W]	4	N/A
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAR Query on PAR Download:Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	PAROMOMYCIN C₂₃ H₄₅ N₅ O₁₄ UOZODPSAJZTQNH-LSWIJEOBSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain DE [auth N] SDF format, chain BE [auth D] MOL2 format, chain DE [auth N] MOL2 format, chain BE [auth D] mmCIF format, chain DE [auth N] mmCIF format, chain BE [auth D]	BE [auth D], DE [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BE [auth D] Focus chain DE [auth N] Interactions & Density Focus chain BE [auth D] Focus chain DE [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain BC [auth A] SDF format, chain BD [auth A] SDF format, chain CA [auth A] SDF format, chain CC [auth A] SDF format, chain CD [auth A] SDF format, chain CE [auth J] SDF format, chain DA [auth A] SDF format, chain DB [auth A] SDF format, chain EA [auth A] SDF format, chain EB [auth A] SDF format, chain FC [auth A] SDF format, chain FD [auth A] SDF format, chain GA [auth A] SDF format, chain GC [auth A] SDF format, chain HB [auth A] SDF format, chain HC [auth A] SDF format, chain IA [auth A] SDF format, chain IB [auth A] SDF format, chain IC [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth A] SDF format, chain JC [auth A] SDF format, chain KC [auth A] SDF format, chain KD [auth A] SDF format, chain LA [auth A] SDF format, chain LB [auth A] SDF format, chain LD [auth A] SDF format, chain MB [auth A] SDF format, chain MC [auth A] SDF format, chain NA [auth A] SDF format, chain NB [auth A] SDF format, chain NC [auth A] SDF format, chain ND [auth A] SDF format, chain OA [auth A] SDF format, chain OC [auth A] SDF format, chain PA [auth A] SDF format, chain PB [auth A] SDF format, chain PC [auth A] SDF format, chain PD [auth A] SDF format, chain QB [auth A] SDF format, chain RA [auth A] SDF format, chain RC [auth A] SDF format, chain RD [auth A] SDF format, chain SA [auth A] SDF format, chain SB [auth A] SDF format, chain SD [auth A] SDF format, chain TA [auth A] SDF format, chain TB [auth A] SDF format, chain TC [auth A] SDF format, chain TD [auth A] SDF format, chain UA [auth A] SDF format, chain VB [auth A] SDF format, chain WA [auth A] SDF format, chain WB [auth A] SDF format, chain XA [auth A] SDF format, chain XC [auth A] SDF format, chain Y [auth A] SDF format, chain YD [auth X] SDF format, chain ZD [auth X] SDF format, chain ZC [auth A] SDF format, chain ZB [auth A] SDF format, chain ZA [auth A] SDF format, chain Z [auth A] SDF format, chain YC [auth A] SDF format, chain YB [auth A] SDF format, chain YA [auth A] SDF format, chain XD [auth A] SDF format, chain XB [auth A] SDF format, chain WD [auth A] SDF format, chain WC [auth A] SDF format, chain VD [auth A] SDF format, chain VC [auth A] SDF format, chain VA [auth A] SDF format, chain UD [auth A] SDF format, chain UC [auth A] SDF format, chain UB [auth A] SDF format, chain SC [auth A] SDF format, chain RB [auth A] SDF format, chain QD [auth A] SDF format, chain QC [auth A] SDF format, chain QA [auth A] SDF format, chain OD [auth A] SDF format, chain OB [auth A] SDF format, chain MD [auth A] SDF format, chain MA [auth A] SDF format, chain LC [auth A] SDF format, chain KB [auth A] SDF format, chain KA [auth A] SDF format, chain JD [auth A] SDF format, chain ID [auth A] SDF format, chain HD [auth A] SDF format, chain HA [auth A] SDF format, chain GD [auth A] SDF format, chain GB [auth A] SDF format, chain FB [auth A] SDF format, chain FA [auth A] SDF format, chain ED [auth A] SDF format, chain EC [auth A] SDF format, chain DD [auth A] SDF format, chain DC [auth A] SDF format, chain CB [auth A] SDF format, chain BB [auth A] SDF format, chain BA [auth A] SDF format, chain AE [auth X] SDF format, chain AD [auth A] SDF format, chain AC [auth A] SDF format, chain AA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BC [auth A] MOL2 format, chain BD [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CC [auth A] MOL2 format, chain CD [auth A] MOL2 format, chain CE [auth J] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain FC [auth A] MOL2 format, chain FD [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GC [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain HC [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain IC [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain JC [auth A] MOL2 format, chain KC [auth A] MOL2 format, chain KD [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth A] MOL2 format, chain LD [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain MC [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth A] MOL2 format, chain NC [auth A] MOL2 format, chain ND [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain OC [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth A] MOL2 format, chain PC [auth A] MOL2 format, chain PD [auth A] MOL2 format, chain QB [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain RC [auth A] MOL2 format, chain RD [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth A] MOL2 format, chain SD [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth A] MOL2 format, chain TC [auth A] MOL2 format, chain TD [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VB [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain XC [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YD [auth X] MOL2 format, chain ZD [auth X] MOL2 format, chain ZC [auth A] MOL2 format, chain ZB [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain YC [auth A] MOL2 format, chain YB [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain XD [auth A] MOL2 format, chain XB [auth A] MOL2 format, chain WD [auth A] MOL2 format, chain WC [auth A] MOL2 format, chain VD [auth A] MOL2 format, chain VC [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain UD [auth A] MOL2 format, chain UC [auth A] MOL2 format, chain UB [auth A] MOL2 format, chain SC [auth A] MOL2 format, chain RB [auth A] MOL2 format, chain QD [auth A] MOL2 format, chain QC [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain OD [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain MD [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LC [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain JD [auth A] MOL2 format, chain ID [auth A] MOL2 format, chain HD [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain GD [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain ED [auth A] MOL2 format, chain EC [auth A] MOL2 format, chain DD [auth A] MOL2 format, chain DC [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AE [auth X] MOL2 format, chain AD [auth A] MOL2 format, chain AC [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain BC [auth A] mmCIF format, chain BD [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CC [auth A] mmCIF format, chain CD [auth A] mmCIF format, chain CE [auth J] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain FC [auth A] mmCIF format, chain FD [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain GC [auth A] mmCIF format, chain HB [auth A] mmCIF format, chain HC [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth A] mmCIF format, chain IC [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth A] mmCIF format, chain JC [auth A] mmCIF format, chain KC [auth A] mmCIF format, chain KD [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth A] mmCIF format, chain LD [auth A] mmCIF format, chain MB [auth A] mmCIF format, chain MC [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth A] mmCIF format, chain NC [auth A] mmCIF format, chain ND [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain OC [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth A] mmCIF format, chain PC [auth A] mmCIF format, chain PD [auth A] mmCIF format, chain QB [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain RC [auth A] mmCIF format, chain RD [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth A] mmCIF format, chain SD [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth A] mmCIF format, chain TC [auth A] mmCIF format, chain TD [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain VB [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain WB [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain XC [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YD [auth X] mmCIF format, chain ZD [auth X] mmCIF format, chain ZC [auth A] mmCIF format, chain ZB [auth A] mmCIF format, chain ZA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain YC [auth A] mmCIF format, chain YB [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain XD [auth A] mmCIF format, chain XB [auth A] mmCIF format, chain WD [auth A] mmCIF format, chain WC [auth A] mmCIF format, chain VD [auth A] mmCIF format, chain VC [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain UD [auth A] mmCIF format, chain UC [auth A] mmCIF format, chain UB [auth A] mmCIF format, chain SC [auth A] mmCIF format, chain RB [auth A] mmCIF format, chain QD [auth A] mmCIF format, chain QC [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain OD [auth A] mmCIF format, chain OB [auth A] mmCIF format, chain MD [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LC [auth A] mmCIF format, chain KB [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain JD [auth A] mmCIF format, chain ID [auth A] mmCIF format, chain HD [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain GD [auth A] mmCIF format, chain GB [auth A] mmCIF format, chain FB [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain ED [auth A] mmCIF format, chain EC [auth A] mmCIF format, chain DD [auth A] mmCIF format, chain DC [auth A] mmCIF format, chain CB [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AE [auth X] mmCIF format, chain AD [auth A] mmCIF format, chain AC [auth A] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth A] AC [auth A] AD [auth A] AE [auth X] AA [auth A], AB [auth A], AC [auth A], AD [auth A], AE [auth X], BA [auth A], BB [auth A], BC [auth A], BD [auth A], CA [auth A], CB [auth A], CC [auth A], CD [auth A], CE [auth J], DA [auth A], DB [auth A], DC [auth A], DD [auth A], EA [auth A], EB [auth A], EC [auth A], ED [auth A], FA [auth A], FB [auth A], FC [auth A], FD [auth A], GA [auth A], GB [auth A], GC [auth A], GD [auth A], HA [auth A], HB [auth A], HC [auth A], HD [auth A], IA [auth A], IB [auth A], IC [auth A], ID [auth A], JA [auth A], JB [auth A], JC [auth A], JD [auth A], KA [auth A], KB [auth A], KC [auth A], KD [auth A], LA [auth A], LB [auth A], LC [auth A], LD [auth A], MA [auth A], MB [auth A], MC [auth A], MD [auth A], NA [auth A], NB [auth A], NC [auth A], ND [auth A], OA [auth A], OB [auth A], OC [auth A], OD [auth A], PA [auth A], PB [auth A], PC [auth A], PD [auth A], QA [auth A], QB [auth A], QC [auth A], QD [auth A], RA [auth A], RB [auth A], RC [auth A], RD [auth A], SA [auth A], SB [auth A], SC [auth A], SD [auth A], TA [auth A], TB [auth A], TC [auth A], TD [auth A], UA [auth A], UB [auth A], UC [auth A], UD [auth A], VA [auth A], VB [auth A], VC [auth A], VD [auth A], WA [auth A], WB [auth A], WC [auth A], WD [auth A], XA [auth A], XB [auth A], XC [auth A], XD [auth A], Y [auth A], YA [auth A], YB [auth A], YC [auth A], YD [auth X], Z [auth A], ZA [auth A], ZB [auth A], ZC [auth A], ZD [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth A] Focus chain AD [auth A] Focus chain AE [auth X] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain BC [auth A] Focus chain BD [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain CC [auth A] Focus chain CD [auth A] Focus chain CE [auth J] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain DC [auth A] Focus chain DD [auth A] Focus chain EA [auth A] Focus chain EB [auth A] Focus chain EC [auth A] Focus chain ED [auth A] Focus chain FA [auth A] Focus chain FB [auth A] Focus chain FC [auth A] Focus chain FD [auth A] Focus chain GA [auth A] Focus chain GB [auth A] Focus chain GC [auth A] Focus chain GD [auth A] Focus chain HA [auth A] Focus chain HB [auth A] Focus chain HC [auth A] Focus chain HD [auth A] Focus chain IA [auth A] Focus chain IB [auth A] Focus chain IC [auth A] Focus chain ID [auth A] Focus chain JA [auth A] Focus chain JB [auth A] Focus chain JC [auth A] Focus chain JD [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain KC [auth A] Focus chain KD [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LC [auth A] Focus chain LD [auth A] Focus chain MA [auth A] Focus chain MB [auth A] Focus chain MC [auth A] Focus chain MD [auth A] Focus chain NA [auth A] Focus chain NB [auth A] Focus chain NC [auth A] Focus chain ND [auth A] Focus chain OA [auth A] Focus chain OB [auth A] Focus chain OC [auth A] Focus chain OD [auth A] Focus chain PA [auth A] Focus chain PB [auth A] Focus chain PC [auth A] Focus chain PD [auth A] Focus chain QA [auth A] Focus chain QB [auth A] Focus chain QC [auth A] Focus chain QD [auth A] Focus chain RA [auth A] Focus chain RB [auth A] Focus chain RC [auth A] Focus chain RD [auth A] Focus chain SA [auth A] Focus chain SB [auth A] Focus chain SC [auth A] Focus chain SD [auth A] Focus chain TA [auth A] Focus chain TB [auth A] Focus chain TC [auth A] Focus chain TD [auth A] Focus chain UA [auth A] Focus chain UB [auth A] Focus chain UC [auth A] Focus chain UD [auth A] Focus chain VA [auth A] Focus chain VB [auth A] Focus chain VC [auth A] Focus chain VD [auth A] Focus chain WA [auth A] Focus chain WB [auth A] Focus chain WC [auth A] Focus chain WD [auth A] Focus chain XA [auth A] Focus chain XB [auth A] Focus chain XC [auth A] Focus chain XD [auth A] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth A] Focus chain YC [auth A] Focus chain YD [auth X] Focus chain Z [auth A] Focus chain ZA [auth A] Focus chain ZB [auth A] Focus chain ZC [auth A] Focus chain ZD [auth X] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth A] Focus chain AD [auth A] Focus chain AE [auth X] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain BC [auth A] Focus chain BD [auth A] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain CC [auth A] Focus chain CD [auth A] Focus chain CE [auth J] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain DC [auth A] Focus chain DD [auth A] Focus chain EA [auth A] Focus chain EB [auth A] Focus chain EC [auth A] Focus chain ED [auth A] Focus chain FA [auth A] Focus chain FB [auth A] Focus chain FC [auth A] Focus chain FD [auth A] Focus chain GA [auth A] Focus chain GB [auth A] Focus chain GC [auth A] Focus chain GD [auth A] Focus chain HA [auth A] Focus chain HB [auth A] Focus chain HC [auth A] Focus chain HD [auth A] Focus chain IA [auth A] Focus chain IB [auth A] Focus chain IC [auth A] Focus chain ID [auth A] Focus chain JA [auth A] Focus chain JB [auth A] Focus chain JC [auth A] Focus chain JD [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain KC [auth A] Focus chain KD [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LC [auth A] Focus chain LD [auth A] Focus chain MA [auth A] Focus chain MB [auth A] Focus chain MC [auth A] Focus chain MD [auth A] Focus chain NA [auth A] Focus chain NB [auth A] Focus chain NC [auth A] Focus chain ND [auth A] Focus chain OA [auth A] Focus chain OB [auth A] Focus chain OC [auth A] Focus chain OD [auth A] Focus chain PA [auth A] Focus chain PB [auth A] Focus chain PC [auth A] Focus chain PD [auth A] Focus chain QA [auth A] Focus chain QB [auth A] Focus chain QC [auth A] Focus chain QD [auth A] Focus chain RA [auth A] Focus chain RB [auth A] Focus chain RC [auth A] Focus chain RD [auth A] Focus chain SA [auth A] Focus chain SB [auth A] Focus chain SC [auth A] Focus chain SD [auth A] Focus chain TA [auth A] Focus chain TB [auth A] Focus chain TC [auth A] Focus chain TD [auth A] Focus chain UA [auth A] Focus chain UB [auth A] Focus chain UC [auth A] Focus chain UD [auth A] Focus chain VA [auth A] Focus chain VB [auth A] Focus chain VC [auth A] Focus chain VD [auth A] Focus chain WA [auth A] Focus chain WB [auth A] Focus chain WC [auth A] Focus chain WD [auth A] Focus chain XA [auth A] Focus chain XB [auth A] Focus chain XC [auth A] Focus chain XD [auth A] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth A] Focus chain YC [auth A] Focus chain YD [auth X] Focus chain Z [auth A] Focus chain ZA [auth A] Focus chain ZB [auth A] Focus chain ZC [auth A] Focus chain ZD [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.273 (Depositor), 0.256 (DCC)
R-Value Work: 0.227 (Depositor), 0.216 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 401.122	α = 90
b = 401.122	β = 90
c = 175.899	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-12-14

Deposition Author(s):

Murphy, F.V.

Ramakrishnan, V.

Revision History (Full details and data files)

Version 1.0: 2004-12-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.4: 2024-11-13
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

1XNR | pdb_00001xnr

Crystal Structure of an Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center

Literature

Structure of a purine-purine wobble base pair in the decoding center of the ribosome.

Biological Assembly 1

Macromolecules

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