4WOI

4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.174 

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This is version 1.3 of the entry. See complete history


Literature

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions.

Wasserman, M.R.Pulk, A.Zhou, Z.Altman, R.B.Zinder, J.C.Green, K.D.Garneau-Tsodikova, S.Doudna Cate, J.H.Blanchard, S.C.

(2015) Nat Commun 6: 7896-7896

  • DOI: 10.1038/ncomms8896
  • Primary Citation of Related Structures:  
    4WOI

  • PubMed Abstract: 
  • Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation ...

    Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6'-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6'-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the 6'-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation.


    Organizational Affiliation

    1] Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA [2] Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB],
KC [auth DB]
241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC],
LC [auth DC]
233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD],
MC [auth DD]
206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE],
NC [auth DE]
167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF],
OC [auth DF]
135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG],
PC [auth DG]
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH],
QC [auth DH]
130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 9
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30S ribosomal protein S9I [auth AI],
RC [auth DI]
130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 10
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30S ribosomal protein S10J [auth AJ],
SC [auth DJ]
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK],
TC [auth DK]
129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 12
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30S ribosomal protein S12L [auth AL],
UC [auth DL]
124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 13
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30S ribosomal protein S13M [auth AM],
VC [auth DM]
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 14
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30S ribosomal protein S14N [auth AN],
WC [auth DN]
101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 15
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30S ribosomal protein S15O [auth AO],
XC [auth DO]
89Escherichia coli O157:H7 str. TW14359Mutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP],
YC [auth DP]
82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 17
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30S ribosomal protein S17Q [auth AQ],
ZC [auth DQ]
84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 18
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30S ribosomal protein S18R [auth AR],
AD [auth DR]
75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 19
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30S ribosomal protein S19S [auth AS],
BD [auth DS]
92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 20
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30S ribosomal protein S20T [auth AT],
CD [auth DT]
87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 21
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30S ribosomal protein S21U [auth AU],
DD [auth DU]
71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 22
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Ribosome-recycling factorV [auth AV]185Escherichia coli K-12Mutation(s): 0 
Gene Names: frrrrfb0172JW0167
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth BC],
GB [auth CC]
273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 28
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50S ribosomal protein L3BA [auth BD],
HB [auth CD]
209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 29
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50S ribosomal protein L4CA [auth BE],
IB [auth CE]
201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 30
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50S ribosomal protein L5DA [auth BF],
JB [auth CF]
179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 31
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50S ribosomal protein L6EA [auth BG],
KB [auth CG]
177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 32
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50S ribosomal protein L9FA [auth BH],
LB [auth CH]
149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11GA [auth BI],
MB [auth CI]
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 34
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50S ribosomal protein L13HA [auth BJ],
NB [auth CJ]
142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 35
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50S ribosomal protein L14IA [auth BK],
OB [auth CK]
123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 36
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50S ribosomal protein L15JA [auth BL],
PB [auth CL]
144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 37
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50S ribosomal protein L16KA [auth BM],
QB [auth CM]
136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 38
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50S ribosomal protein L17LA [auth BN],
RB [auth CN]
127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 39
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50S ribosomal protein L18MA [auth BO],
SB [auth CO]
117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 40
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50S ribosomal protein L19NA [auth BP],
TB [auth CP]
115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 41
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50S ribosomal protein L20OA [auth BQ],
UB [auth CQ]
118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 42
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50S ribosomal protein L21PA [auth BR],
VB [auth CR]
103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 43
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50S ribosomal protein L22QA [auth BS],
WB [auth CS]
110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 44
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50S ribosomal protein L23RA [auth BT],
XB [auth CT]
100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24SA [auth BU],
YB [auth CU]
104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25TA [auth BV],
ZB [auth CV]
94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27UA [auth BW],
AC [auth CW]
85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28VA [auth BX],
BC [auth CX]
78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29WA [auth BY],
CC [auth CY]
63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30XA [auth BZ],
DC [auth CZ]
59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32YA [auth B0],
EC [auth C0]
57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33ZA [auth B1],
FC [auth C1]
55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth B2],
GC [auth C2]
46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth B3],
HC [auth C3]
65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth B4],
IC [auth C4]
38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1DB [auth B5]228Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth AA],
JC [auth DA]
1542Escherichia coli str. K-12 substr. MDS42
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Entity ID: 23
MoleculeChainsLengthOrganismImage
Messenger RNAW [auth AW],
ED [auth DV]
16Enterobacteria phage L1
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Entity ID: 24
MoleculeChainsLengthOrganismImage
Phenylalanine specific transfer RNA, tRNA-PheX [auth AX],
FD [auth DW]
76Escherichia coli str. K-12 substr. MDS42
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Entity ID: 25
MoleculeChainsLengthOrganismImage
23S ribosomal RNAY [auth BA],
EB [auth CA]
2904Escherichia coli str. K-12 substr. MDS42
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Entity ID: 26
MoleculeChainsLengthOrganismImage
5S ribosomal RNAZ [auth BB],
FB [auth CB]
120Escherichia coli str. K-12 substr. MDS42
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
BG [auth BA],
CG [auth BA],
DG [auth BA],
EG [auth BA],
FG [auth BA],
BG [auth BA],
CG [auth BA],
DG [auth BA],
EG [auth BA],
FG [auth BA],
FU [auth CA],
GU [auth CA],
HU [auth CA],
IU [auth CA],
JU [auth CA],
RW [auth DA],
SW [auth DA],
ZF [auth AA]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
PU [auth C4],
VN [auth B4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AA],
AF [auth AA],
AG [auth AN],
AH [auth BA],
AI [auth BA],
AE [auth AA],
AF [auth AA],
AG [auth AN],
AH [auth BA],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AL [auth BA],
AM [auth BA],
AN [auth BA],
AO [auth CA],
AP [auth CA],
AQ [auth CA],
AR [auth CA],
AS [auth CA],
AT [auth CA],
AU [auth CA],
AV [auth DA],
AW [auth DA],
BE [auth AA],
BF [auth AA],
BH [auth BA],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth BA],
BM [auth BA],
BN [auth BA],
BO [auth CA],
BP [auth CA],
BQ [auth CA],
BR [auth CA],
BS [auth CA],
BT [auth CA],
BU [auth CA],
BV [auth DA],
BW [auth DA],
CE [auth AA],
CF [auth AA],
CH [auth BA],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth BA],
CM [auth BA],
CN [auth BA],
CO [auth CA],
CP [auth CA],
CQ [auth CA],
CR [auth CA],
CS [auth CA],
CT [auth CA],
CU [auth CA],
CV [auth DA],
CW [auth DA],
DE [auth AA],
DF [auth AA],
DH [auth BA],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth BA],
DM [auth BA],
DN [auth BA],
DO [auth CA],
DP [auth CA],
DQ [auth CA],
DR [auth CA],
DS [auth CA],
DT [auth CA],
DU [auth CA],
DV [auth DA],
DW [auth DA],
EE [auth AA],
EF [auth AA],
EH [auth BA],
EI [auth BA],
EJ [auth BA],
EK [auth BA],
EL [auth BA],
EM [auth BA],
EN [auth BA],
EO [auth CA],
EP [auth CA],
EQ [auth CA],
ER [auth CA],
ES [auth CA],
ET [auth CA],
EU [auth CA],
EV [auth DA],
EW [auth DA],
FE [auth AA],
FF [auth AA],
FH [auth BA],
FI [auth BA],
FJ [auth BA],
FK [auth BA],
FL [auth BA],
FM [auth BA],
FN [auth BA],
FO [auth CA],
FP [auth CA],
FQ [auth CA],
FR [auth CA],
FS [auth CA],
FT [auth CA],
FV [auth DA],
FW [auth DA],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth BA],
GH [auth BA],
GI [auth BA],
GJ [auth BA],
GK [auth BA],
GL [auth BA],
GM [auth BA],
GN [auth BA],
GO [auth CA],
GP [auth CA],
GQ [auth CA],
GR [auth CA],
GS [auth CA],
GT [auth CA],
GV [auth DA],
GW [auth DA],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth BA],
HH [auth BA],
HI [auth BA],
HJ [auth BA],
HK [auth BA],
HL [auth BA],
HM [auth BA],
HN [auth BA],
HO [auth CA],
HP [auth CA],
HQ [auth CA],
HR [auth CA],
HS [auth CA],
HT [auth CA],
HV [auth DA],
HW [auth DA],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth BA],
IH [auth BA],
II [auth BA],
IJ [auth BA],
IK [auth BA],
IL [auth BA],
IM [auth BA],
IN [auth BA],
IO [auth CA],
IP [auth CA],
IQ [auth CA],
IR [auth CA],
IS [auth CA],
IT [auth CA],
IV [auth DA],
IW [auth DA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth BA],
JH [auth BA],
JI [auth BA],
JJ [auth BA],
JK [auth BA],
JL [auth BA],
JM [auth BA],
JN [auth BA],
JO [auth CA],
JP [auth CA],
JQ [auth CA],
JR [auth CA],
JS [auth CA],
JT [auth CA],
JV [auth DA],
JW [auth DA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth BA],
KH [auth BA],
KI [auth BA],
KJ [auth BA],
KK [auth BA],
KL [auth BA],
KM [auth BA],
KN [auth BA],
KO [auth CA],
KP [auth CA],
KQ [auth CA],
KR [auth CA],
KS [auth CA],
KT [auth CA],
KU [auth CB],
KV [auth DA],
KW [auth DA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth BA],
LH [auth BA],
LI [auth BA],
LJ [auth BA],
LK [auth BA],
LL [auth BA],
LM [auth BA],
LN [auth BA],
LO [auth CA],
LP [auth CA],
LQ [auth CA],
LR [auth CA],
LS [auth CA],
LT [auth CA],
LU [auth CB],
LV [auth DA],
LW [auth DA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
MG [auth BA],
MH [auth BA],
MI [auth BA],
MJ [auth BA],
MK [auth BA],
ML [auth BA],
MM [auth BA],
MN [auth BA],
MO [auth CA],
MP [auth CA],
MQ [auth CA],
MR [auth CA],
MS [auth CA],
MT [auth CA],
MU [auth CB],
MV [auth DA],
MW [auth DA],
ND [auth AA],
NE [auth AA],
NF [auth AA],
NG [auth BA],
NH [auth BA],
NI [auth BA],
NJ [auth BA],
NK [auth BA],
NL [auth BA],
NM [auth BA],
NN [auth BB],
NO [auth CA],
NP [auth CA],
NQ [auth CA],
NR [auth CA],
NS [auth CA],
NT [auth CA],
NU [auth CD],
NV [auth DA],
NW [auth DA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
OG [auth BA],
OH [auth BA],
OI [auth BA],
OJ [auth BA],
OK [auth BA],
OL [auth BA],
OM [auth BA],
ON [auth BB],
OO [auth CA],
OP [auth CA],
OQ [auth CA],
OR [auth CA],
OS [auth CA],
OT [auth CA],
OU [auth CQ],
OV [auth DA],
OW [auth DA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
PG [auth BA],
PH [auth BA],
PI [auth BA],
PJ [auth BA],
PK [auth BA],
PL [auth BA],
PM [auth BA],
PN [auth BB],
PO [auth CA],
PP [auth CA],
PQ [auth CA],
PR [auth CA],
PS [auth CA],
PT [auth CA],
PV [auth DA],
PW [auth DA],
QD [auth AA],
QE [auth AA],
QF [auth AA],
QG [auth BA],
QH [auth BA],
QI [auth BA],
QJ [auth BA],
QK [auth BA],
QL [auth BA],
QM [auth BA],
QN [auth BB],
QO [auth CA],
QP [auth CA],
QQ [auth CA],
QR [auth CA],
QS [auth CA],
QT [auth CA],
QU [auth DA],
QV [auth DA],
QW [auth DA],
RD [auth AA],
RE [auth AA],
RF [auth AA],
RG [auth BA],
RH [auth BA],
RI [auth BA],
RJ [auth BA],
RK [auth BA],
RL [auth BA],
RM [auth BA],
RN [auth BL],
RO [auth CA],
RP [auth CA],
RQ [auth CA],
RR [auth CA],
RS [auth CA],
RT [auth CA],
RU [auth DA],
RV [auth DA],
SD [auth AA],
SE [auth AA],
SF [auth AA],
SG [auth BA],
SH [auth BA],
SI [auth BA],
SJ [auth BA],
SK [auth BA],
SL [auth BA],
SM [auth BA],
SN [auth BL],
SO [auth CA],
SP [auth CA],
SQ [auth CA],
SR [auth CA],
SS [auth CA],
ST [auth CA],
SU [auth DA],
SV [auth DA],
TD [auth AA],
TE [auth AA],
TF [auth AA],
TG [auth BA],
TH [auth BA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth BA],
TM [auth BA],
TN [auth BO],
TO [auth CA],
TP [auth CA],
TQ [auth CA],
TR [auth CA],
TS [auth CA],
TT [auth CA],
TU [auth DA],
TV [auth DA],
TW [auth DD],
UD [auth AA],
UE [auth AA],
UF [auth AA],
UG [auth BA],
UH [auth BA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth BA],
UM [auth BA],
UN [auth BQ],
UO [auth CA],
UP [auth CA],
UQ [auth CA],
UR [auth CA],
US [auth CA],
UT [auth CA],
UU [auth DA],
UV [auth DA],
UW [auth DD],
VD [auth AA],
VE [auth AA],
VF [auth AA],
VG [auth BA],
VH [auth BA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth BA],
VM [auth BA],
VO [auth CA],
VP [auth CA],
VQ [auth CA],
VR [auth CA],
VS [auth CA],
VT [auth CA],
VU [auth DA],
VV [auth DA],
VW [auth DN],
WD [auth AA],
WE [auth AA],
WF [auth AA],
WG [auth BA],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth BA],
WM [auth BA],
WN [auth CA],
WO [auth CA],
WP [auth CA],
WQ [auth CA],
WR [auth CA],
WS [auth CA],
WT [auth CA],
WU [auth DA],
WV [auth DA],
XD [auth AA],
XE [auth AA],
XF [auth AA],
XG [auth BA],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XK [auth BA],
XL [auth BA],
XM [auth BA],
XN [auth CA],
XO [auth CA],
XP [auth CA],
XQ [auth CA],
XR [auth CA],
XS [auth CA],
XT [auth CA],
XU [auth DA],
XV [auth DA],
YD [auth AA],
YE [auth AA],
YF [auth AA],
YG [auth BA],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YK [auth BA],
YL [auth BA],
YM [auth BA],
YN [auth CA],
YO [auth CA],
YP [auth CA],
YQ [auth CA],
YR [auth CA],
YS [auth CA],
YT [auth CA],
YU [auth DA],
YV [auth DA],
ZD [auth AA],
ZE [auth AA],
ZG [auth BA],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZK [auth BA],
ZL [auth BA],
ZM [auth BA],
ZN [auth CA],
ZO [auth CA],
ZP [auth CA],
ZQ [auth CA],
ZR [auth CA],
ZS [auth CA],
ZT [auth CA],
ZU [auth DA],
ZV [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.1α = 90
b = 435.24β = 90
c = 614.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R01GM079238
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM65050
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI090048
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA92584
Human Frontiers in Science ProgramUnited StatesRGY0088
National Science Foundation (NSF, United States)United States0644129
Department of Energy (DOE, United States)United StatesDE-AC0376SF00098

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence