5LI0

70S ribosome from Staphylococcus aureus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the 70S ribosome from human pathogen Staphylococcus aureus.

Khusainov, I.Vicens, Q.Bochler, A.Grosse, F.Myasnikov, A.Menetret, J.F.Chicher, J.Marzi, S.Romby, P.Yusupova, G.Yusupov, M.Hashem, Y.

(2016) Nucleic Acids Res 44: 10491-10504

  • DOI: 10.1093/nar/gkw933
  • Primary Citation of Related Structures:  
    5LI0

  • PubMed Abstract: 
  • Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the importance of such features may be less obvious within more closely related organisms, their existence could account for vital yet species-specific mechanisms of translation regulation that would involve stalling, cell survival and antibiotic resistance ...

    Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the importance of such features may be less obvious within more closely related organisms, their existence could account for vital yet species-specific mechanisms of translation regulation that would involve stalling, cell survival and antibiotic resistance. Here, we present the first full 70S ribosome structure from Staphylococcus aureus, a Gram-positive pathogenic bacterium, solved by cryo-electron microscopy. Comparative analysis with other known bacterial ribosomes pinpoints several unique features specific to S. aureus around a conserved core, at both the protein and the RNA levels. Our work provides the structural basis for the many studies aiming at understanding translation regulation in S. aureus and for designing drugs against this often multi-resistant pathogen.


    Organizational Affiliation

    Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France y.hashem@ibmc-cnrs.unistra.fr.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]255Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsBSAOUHSC_01232
UniProt
Find proteins for Q2FZ25 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth c]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsCSAOUHSC_02506
UniProt
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]199Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsDSAOUHSC_01829
UniProt
Find proteins for Q2FXK6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]165Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsESAOUHSC_02494
UniProt
Find proteins for Q2FW23 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]96Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsFSAOUHSC_00348
UniProt
Find proteins for Q2G113 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]150Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsGSAOUHSC_00528
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Find proteins for P48940 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]131Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsHSAOUHSC_02498
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]128Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsISAOUHSC_02477
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Find proteins for Q2FW39 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 10
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30S ribosomal protein S10J [auth j]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q931G5 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsKSAOUHSC_02486
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Find proteins for Q2FW31 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]135Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: rpsLSACOL0591
UniProt
Find proteins for Q5HID0 (Staphylococcus aureus (strain COL))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsMSAOUHSC_02487
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth n]60Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsZrpsN1SAOUHSC_02499
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth o]88Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsOSAOUHSC_01250
UniProt
Find proteins for Q2G2Q1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]90Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsPSAOUHSC_01208
UniProt
Find proteins for Q2FZ45 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]86Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsQSAOUHSC_02503
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Find proteins for Q2FW15 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]71Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsRSAOUHSC_00350
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]84Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsSSAOUHSC_02508
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpsTSAOUHSC_01689
UniProt
Find proteins for Q2FXY6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2W [auth D]275Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplBSAOUHSC_02509
UniProt
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3X [auth E]218Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplCSAOUHSC_02512
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4Y [auth F]199Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplDSAOUHSC_02511
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5Z [auth G]166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplESAOUHSC_02500
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6AA [auth H]164Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplFSAOUHSC_02496
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13BA [auth M]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplMSAOUHSC_02478
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Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 29
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50S ribosomal protein L14CA [auth N]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplNSAOUHSC_02502
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Entity ID: 30
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50S ribosomal protein L15DA [auth O]131Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplOSAOUHSC_02492
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16EA [auth P]141Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplPSAOUHSC_02505
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Entity ID: 32
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50S ribosomal protein L17FA [auth Q]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplQSAOUHSC_02484
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Entity ID: 33
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50S ribosomal protein L18GA [auth R]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplRSAOUHSC_02495
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Entity ID: 34
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50S ribosomal protein L19HA [auth S]110Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplSSAOUHSC_01211
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Entity ID: 35
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50S ribosomal protein L20IA [auth T]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplTSAOUHSC_01784
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Entity ID: 36
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50S ribosomal protein L21JA [auth U]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplUSAOUHSC_01757
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Entity ID: 37
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50S ribosomal protein L22KA [auth V]112Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplVSAOUHSC_02507
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Entity ID: 38
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50S ribosomal protein L23LA [auth W]89Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplWSAOUHSC_02510
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Entity ID: 39
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50S ribosomal protein L24MA [auth X]100Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplXSAOUHSC_02501
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Entity ID: 40
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50S ribosomal protein L25NA [auth Y]94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplYctcSAOUHSC_00474
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Entity ID: 41
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50S ribosomal protein L27OA [auth Z]82Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmASAOUHSC_01755
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Entity ID: 42
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50S ribosomal protein L28PA [auth 0]46Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmBSAOUHSC_01191
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29QA [auth 1]65Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmCSAOUHSC_02504
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Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30RA [auth 2]57Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmDSAOUHSC_02493
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Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BSA [auth 3]84Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmE2SAOUHSC_02361
UniProt
Find proteins for Q2FWD8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32TA [auth 4]56Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmFSAOUHSC_01078
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Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 2UA [auth 5]39Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmG2SAOUHSC_01651
UniProt
Find proteins for Q2FY22 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34VA [auth 6]44Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmHSAOUHSC_03055
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Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35WA [auth 7]60Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmISAOUHSC_01785
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36XA [auth 8]37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmJSAOUHSC_02488
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Find proteins for Q2FW29 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth a]1547Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 21
MoleculeChainsLengthOrganismImage
23S ribosomal RNAU [auth A]2918Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 22
MoleculeChainsLengthOrganismImage
5S ribosomal RNAV [auth B]114Staphylococcus aureus subsp. aureus NCTC 8325
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MC [auth 8]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth A],
AC [auth A],
BB [auth A],
BC [auth A],
CB [auth A],
AB [auth A],
AC [auth A],
BB [auth A],
BC [auth A],
CB [auth A],
CC [auth A],
DC [auth A],
EC [auth A],
FC [auth A],
GC [auth A],
HB [auth A],
HC [auth A],
IC [auth A],
JC [auth A],
KC [auth A],
LC [auth A],
NB [auth A],
OB [auth A],
PB [auth A],
QB [auth A],
RB [auth A],
SB [auth A],
TB [auth A],
UB [auth A],
VB [auth A],
WB [auth A],
XB [auth A],
YA [auth a],
YB [auth A],
ZA [auth a],
ZB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
O
Query on O

Download Ideal Coordinates CCD File 
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth A],
IB [auth A],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth A],
IB [auth A],
JB [auth A],
KB [auth A],
LB [auth A],
MB [auth A]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-11-06
    Changes: Data collection
  • Version 1.3: 2019-12-11
    Changes: Other