4V52

Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.274 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history. 


Literature

Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.

Borovinskaya, M.A., Pai, R.D., Zhang, W., Schuwirth, B.S., Holton, J.M., Hirokawa, G., Kaji, H., Kaji, A., Cate, J.H.

(2007) Nat Struct Mol Biol 14: 727-732

  • DOI: https://doi.org/10.1038/nsmb1271
  • Primary Citation of Related Structures:  
    4V52, 4V53, 4V54, 4V55, 4V5Y

  • PubMed Abstract: 

    Aminoglycosides are widely used antibiotics that cause messenger RNA decoding errors, block mRNA and transfer RNA translocation, and inhibit ribosome recycling. Ribosome recycling follows the termination of protein synthesis and is aided by ribosome recycling factor (RRF) in bacteria. The molecular mechanism by which aminoglycosides inhibit ribosome recycling is unknown. Here we show in X-ray crystal structures of the Escherichia coli 70S ribosome that RRF binding causes RNA helix H69 of the large ribosomal subunit, which is crucial for subunit association, to swing away from the subunit interface. Aminoglycosides bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for aminoglycoside inhibition of ribosome recycling.

    • Organizational Affiliation: 

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth AC],
BB [auth CC]		232Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth AD],
CB [auth CD]		205Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth AE],
DB [auth CE]		166Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth AF],
EB [auth CF]		135Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth AG],
FB [auth CG]		178Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth AH],
GB [auth CH]		129Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth AI],
HB [auth CI]		129Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth AJ],
IB [auth CJ]		103Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth AK],
JB [auth CK]		128Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth AL],
KB [auth CL]		123Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth AM],
LB [auth CM]		117Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14M [auth AN],
MB [auth CN]		100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15N [auth AO],
NB [auth CO]		89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16O [auth AP],
OB [auth CP]		82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17P [auth AQ],
PB [auth CQ]		83Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth AR],
QB [auth CR]		74Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth AS],
RB [auth CS]		91Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth AT],
SB [auth CT]		86Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2T [auth AB],
TB [auth CB]		240Escherichia coliMutation(s): 0 
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30S ribosomal protein S21U [auth AU],
UB [auth CU]		70Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11X [auth BI],
XB [auth DI]		141Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L2Y [auth BC],
YB [auth DC]		272Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth BD],
ZB [auth DD]		209Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14AA [auth BK],
AC [auth DK]		123Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19BA [auth BP],
BC [auth DP]		114Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth BE],
CC [auth DE]		201Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DA [auth BY],
DC [auth DY]		58Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32EA [auth B0],
EC [auth D0]		56Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth B4],
FC [auth D4]		38Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33GA [auth B1],
GC [auth D1]		54Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35HA [auth B3],
HC [auth D3]		64Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25IA [auth BV],
IC [auth DV]		94Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34JA [auth B2],
JC [auth D2]		46Escherichia coliMutation(s): 0 
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50S ribosomal protein L15KA [auth BL],
KC [auth DL]		144Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth BM],
LC [auth DM]		136Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29MA [auth BX],
MC [auth DX]		63Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9NA [auth BH],
NC [auth DH]		149Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13OA [auth BJ],
OC [auth DJ]		142Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17PA [auth BN],
PC [auth DN]		127Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18QA [auth BO],
QC [auth DO]		117Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20RA [auth BQ],
RC [auth DQ]		117Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22SA [auth BS],
SC [auth DS]		110Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth BU],
TC [auth DU]		103Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5UA [auth BF],
UC [auth DF]		178Escherichia coliMutation(s): 0 
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Find proteins for P62399 (Escherichia coli (strain K12))
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UniProt GroupP62399
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6VA [auth BG],
VC [auth DG]		176Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21WA [auth BR],
WC [auth DR]		103Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23XA [auth BT],
XC [auth DT]		100Escherichia coliMutation(s): 0 
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Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28YA [auth BZ],
YC [auth DZ]		78Escherichia coliMutation(s): 0 
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Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27ZA [auth BW],
ZC [auth DW]		84Escherichia coliMutation(s): 0 
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Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth AA],
AB [auth CA]		1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
5S rRNAV [auth BA],
VB [auth DA]		120Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S rRNAW [auth BB],
WB [auth DB]		2,904Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMY
Query on NMY
Download Ideal Coordinates CCD File 
AD [auth AA],
CM [auth DB],
JF [auth BB],
RJ [auth CA]		NEOMYCIN
C23 H46 N6 O13
PGBHMTALBVVCIT-VCIWKGPPSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
KQ [auth D4],
QJ [auth B4]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AE [auth AA]
AF [auth AA]
AG [auth BB]
AH [auth BB]
AI [auth BB]
AE [auth AA],
AF [auth AA],
AG [auth BB],
AH [auth BB],
AI [auth BB],
AJ [auth BB],
AK [auth CA],
AL [auth CA],
AM [auth CE],
AN [auth DB],
AO [auth DB],
AP [auth DB],
AQ [auth DB],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth BB],
BH [auth BB],
BI [auth BB],
BJ [auth BB],
BK [auth CA],
BL [auth CA],
BM [auth CN],
BN [auth DB],
BO [auth DB],
BP [auth DB],
BQ [auth DB],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth BB],
CH [auth BB],
CI [auth BB],
CJ [auth BB],
CK [auth CA],
CL [auth CA],
CN [auth DB],
CO [auth DB],
CP [auth DB],
CQ [auth DB],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth BB],
DH [auth BB],
DI [auth BB],
DJ [auth BB],
DK [auth CA],
DL [auth CA],
DM [auth DB],
DN [auth DB],
DO [auth DB],
DP [auth DB],
DQ [auth DB],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth BB],
EH [auth BB],
EI [auth BB],
EJ [auth BB],
EK [auth CA],
EL [auth CA],
EM [auth DB],
EN [auth DB],
EO [auth DB],
EP [auth DB],
EQ [auth DB],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth BB],
FH [auth BB],
FI [auth BB],
FJ [auth BB],
FK [auth CA],
FL [auth CA],
FM [auth DB],
FN [auth DB],
FO [auth DB],
FP [auth DB],
FQ [auth DB],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth BB],
GH [auth BB],
GI [auth BB],
GJ [auth BB],
GK [auth CA],
GL [auth CA],
GM [auth DB],
GN [auth DB],
GO [auth DB],
GP [auth DB],
GQ [auth DB],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth BB],
HH [auth BB],
HI [auth BB],
HJ [auth BB],
HK [auth CA],
HL [auth CA],
HM [auth DB],
HN [auth DB],
HO [auth DB],
HP [auth DB],
HQ [auth DB],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth BB],
IH [auth BB],
II [auth BB],
IJ [auth BB],
IK [auth CA],
IL [auth CA],
IM [auth DB],
IN [auth DB],
IO [auth DB],
IP [auth DB],
IQ [auth DB],
JD [auth AA],
JE [auth AA],
JG [auth BB],
JH [auth BB],
JI [auth BB],
JJ [auth BB],
JK [auth CA],
JL [auth CA],
JM [auth DB],
JN [auth DB],
JO [auth DB],
JP [auth DB],
JQ [auth DB],
KD [auth AA],
KE [auth AA],
KF [auth BB],
KG [auth BB],
KH [auth BB],
KI [auth BB],
KJ [auth BB],
KK [auth CA],
KL [auth CA],
KM [auth DB],
KN [auth DB],
KO [auth DB],
KP [auth DB],
LD [auth AA],
LE [auth AA],
LF [auth BB],
LG [auth BB],
LH [auth BB],
LI [auth BB],
LJ [auth BB],
LK [auth CA],
LL [auth CA],
LM [auth DB],
LN [auth DB],
LO [auth DB],
LP [auth DB],
MD [auth AA],
ME [auth AA],
MF [auth BB],
MG [auth BB],
MH [auth BB],
MI [auth BB],
MJ [auth BB],
MK [auth CA],
ML [auth CA],
MM [auth DB],
MN [auth DB],
MO [auth DB],
MP [auth DB],
ND [auth AA],
NE [auth AA],
NF [auth BB],
NG [auth BB],
NH [auth BB],
NI [auth BB],
NJ [auth BB],
NK [auth CA],
NL [auth CA],
NM [auth DB],
NN [auth DB],
NO [auth DB],
NP [auth DB],
OD [auth AA],
OE [auth AA],
OF [auth BB],
OG [auth BB],
OH [auth BB],
OI [auth BB],
OJ [auth BB],
OK [auth CA],
OL [auth CA],
OM [auth DB],
ON [auth DB],
OO [auth DB],
OP [auth DB],
PD [auth AA],
PE [auth AA],
PF [auth BB],
PG [auth BB],
PH [auth BB],
PI [auth BB],
PJ [auth BB],
PK [auth CA],
PL [auth CA],
PM [auth DB],
PN [auth DB],
PO [auth DB],
PP [auth DB],
QD [auth AA],
QE [auth AA],
QF [auth BB],
QG [auth BB],
QH [auth BB],
QI [auth BB],
QK [auth CA],
QL [auth CA],
QM [auth DB],
QN [auth DB],
QO [auth DB],
QP [auth DB],
RD [auth AA],
RE [auth AA],
RF [auth BB],
RG [auth BB],
RH [auth BB],
RI [auth BB],
RK [auth CA],
RL [auth CA],
RM [auth DB],
RN [auth DB],
RO [auth DB],
RP [auth DB],
SD [auth AA],
SE [auth AA],
SF [auth BB],
SG [auth BB],
SH [auth BB],
SI [auth BB],
SJ [auth CA],
SK [auth CA],
SL [auth CA],
SM [auth DB],
SN [auth DB],
SO [auth DB],
SP [auth DB],
TD [auth AA],
TE [auth AA],
TF [auth BB],
TG [auth BB],
TH [auth BB],
TI [auth BB],
TJ [auth CA],
TK [auth CA],
TL [auth CA],
TM [auth DB],
TN [auth DB],
TO [auth DB],
TP [auth DB],
UD [auth AA],
UE [auth AA],
UF [auth BB],
UG [auth BB],
UH [auth BB],
UI [auth BB],
UJ [auth CA],
UK [auth CA],
UL [auth CA],
UM [auth DB],
UN [auth DB],
UO [auth DB],
UP [auth DB],
VD [auth AA],
VE [auth AA],
VF [auth BB],
VG [auth BB],
VH [auth BB],
VI [auth BB],
VJ [auth CA],
VK [auth CA],
VL [auth CA],
VM [auth DB],
VN [auth DB],
VO [auth DB],
VP [auth DB],
WD [auth AA],
WE [auth AA],
WF [auth BB],
WG [auth BB],
WH [auth BB],
WI [auth BB],
WJ [auth CA],
WK [auth CA],
WL [auth CA],
WM [auth DB],
WN [auth DB],
WO [auth DB],
WP [auth DB],
XD [auth AA],
XE [auth AA],
XF [auth BB],
XG [auth BB],
XH [auth BB],
XI [auth BB],
XJ [auth CA],
XK [auth CA],
XL [auth CA],
XM [auth DB],
XN [auth DB],
XO [auth DB],
XP [auth DB],
YD [auth AA],
YE [auth AA],
YF [auth BB],
YG [auth BB],
YH [auth BB],
YI [auth BB],
YJ [auth CA],
YK [auth CA],
YL [auth CA],
YM [auth DB],
YN [auth DB],
YO [auth DB],
YP [auth DB],
ZD [auth AA],
ZE [auth AA],
ZF [auth BB],
ZG [auth BB],
ZH [auth BB],
ZI [auth BB],
ZJ [auth CA],
ZK [auth CA],
ZL [auth CA],
ZM [auth DB],
ZN [auth DB],
ZO [auth DB],
ZP [auth DB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.274 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.848α = 90
b = 379.202β = 90
c = 739.283γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description