4V8J

Crystal structure of the bacterial ribosome ram mutation G347U.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

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Literature

Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.

Fagan, C.E., Dunkle, J.A., Maehigashi, T., Dang, M.N., Devaraj, A., Miles, S.J., Qin, D., Fredrick, K., Dunham, C.M.

(2013) Proc Natl Acad Sci U S A 110: 9716-9721

  • DOI: https://doi.org/10.1073/pnas.1301585110
  • Primary Citation of Related Structures:  
    4V8J, 4V97

  • PubMed Abstract: 

    After four decades of research aimed at understanding tRNA selection on the ribosome, the mechanism by which ribosomal ambiguity (ram) mutations promote miscoding remains unclear. Here, we present two X-ray crystal structures of the Thermus thermophilus 70S ribosome containing 16S rRNA ram mutations, G347U and G299A. Each of these mutations causes miscoding in vivo and stimulates elongation factor thermo unstable (EF-Tu)-dependent GTP hydrolysis in vitro. Mutation G299A is located near the interface of ribosomal proteins S4 and S5 on the solvent side of the subunit, whereas G347U is located 77 Å distant, at intersubunit bridge B8, close to where EF-Tu engages the ribosome. Despite these disparate locations, both mutations induce almost identical structural rearrangements that disrupt the B8 bridge--namely, the interaction of h8/h14 with L14 and L19. This conformation most closely resembles that seen upon EF-Tu-GTP-aminoacyl-tRNA binding to the 70S ribosome. These data provide evidence that disruption and/or distortion of B8 is an important aspect of GTPase activation. We propose that, by destabilizing B8, G299A and G347U reduce the energetic cost of attaining the GTPase-activated state and thereby decrease the stringency of decoding. This previously unappreciated role for B8 in controlling the decoding process may hold relevance for many other ribosomal mutations known to influence translational fidelity.

    • Organizational Affiliation: 

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB],
GB [auth CB]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC],
HB [auth CC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD],
IB [auth CD]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE],
JB [auth CE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF],
KB [auth CF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG],
LB [auth CG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH],
MB [auth CH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI],
NB [auth CI]		128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ],
OB [auth CJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK],
PB [auth CK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL],
QB [auth CL]		132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM],
RB [auth CM]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN],
SB [auth CN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO],
TB [auth CO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP],
UB [auth CP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ],
VB [auth CQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR],
WB [auth CR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AS],
XB [auth CS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth AT],
YB [auth CT]		106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein THXU [auth AU],
ZB [auth CU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1BA [auth BC],
GC [auth DC]		229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2CA [auth BD],
HC [auth DD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3DA [auth BE],
IC [auth DE]		206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4EA [auth BF],
JC [auth DF]		210Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5FA [auth BG],
KC [auth DG]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6GA [auth BH],
LC [auth DH]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9HA [auth BI],
MC [auth DI]		148Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13IA [auth BN],
NC [auth DN]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14JA [auth BO],
OC [auth DO]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KA [auth BP],
PC [auth DP]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth BQ],
QC [auth DQ]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MA [auth BR],
RC [auth DR]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18NA [auth BS],
SC [auth DS]		112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OA [auth BT],
TC [auth DT]		146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PA [auth BU],
UC [auth DU]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QA [auth BV],
VC [auth DV]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RA [auth BW],
WC [auth DW]		113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SA [auth BX],
XC [auth DX]		96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth BY],
YC [auth DY]		110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UA [auth BZ],
ZC [auth DZ]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AD [auth D0],
VA [auth B0]		85Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BD [auth D1],
WA [auth B1]		98Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CD [auth D2],
XA [auth B2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DD [auth D3],
YA [auth B3]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31ED [auth D4],
ZA [auth B4]		71Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AB [auth B5],
FD [auth D5]		60Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BB [auth B6],
GD [auth D6]		54Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CB [auth B7],
HD [auth D7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DB [auth B8],
ID [auth D8]		65Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EB [auth B9],
JD [auth D9]		37Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth AA],
FB [auth CA]		1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
tRNA-PheAC [auth CW],
CC [auth CY],
V [auth AW],
X [auth AY]		76Escherichia coli str. K-12 substr. MDS42
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Entity ID: 23
MoleculeChains LengthOrganismImage
tRNA-fMetBC [auth CV],
W [auth AV]		77Escherichia coli str. K-12 substr. MDS42
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Entity ID: 24
MoleculeChains LengthOrganismImage
messenger RNADC [auth CX],
Y [auth AX]		24N/A
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S rRNAEC [auth DA],
Z [auth BA]		2,916Thermus thermophilus HB8
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S rRNAAA [auth BB],
FC [auth DB]		122Thermus thermophilus HB8
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR
Download Ideal Coordinates CCD File 
IV [auth CA],
ZG [auth AA]		PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AH [auth AD],
BH [auth AN],
JV [auth CD],
KV [auth CN]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AAA [auth DA]
ABA [auth DA]
ACA [auth DA]
ADA [auth DA]
AE [auth AA]
AAA [auth DA],
ABA [auth DA],
ACA [auth DA],
ADA [auth DA],
AE [auth AA],
AEA [auth DA],
AF [auth AA],
AFA [auth DA],
AG [auth AA],
AGA [auth D5],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AL [auth BA],
AM [auth BA],
AN [auth BA],
AO [auth BA],
AP [auth BA],
AQ [auth BA],
AR [auth BA],
AS [auth CA],
AT [auth CA],
AU [auth CA],
AV [auth CA],
AW [auth DA],
AX [auth DA],
AY [auth DA],
AZ [auth DA],
BAA [auth DA],
BBA [auth DA],
BCA [auth DA],
BDA [auth DA],
BE [auth AA],
BEA [auth DA],
BF [auth AA],
BFA [auth DA],
BG [auth AA],
BGA [auth D5],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth BA],
BM [auth BA],
BN [auth BA],
BO [auth BA],
BP [auth BA],
BQ [auth BA],
BR [auth BA],
BS [auth CA],
BT [auth CA],
BU [auth CA],
BV [auth CA],
BW [auth DA],
BX [auth DA],
BY [auth DA],
BZ [auth DA],
CAA [auth DA],
CBA [auth DA],
CCA [auth DA],
CDA [auth DA],
CE [auth AA],
CEA [auth DA],
CF [auth AA],
CFA [auth DA],
CG [auth AA],
CH [auth AX],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth BA],
CM [auth BA],
CN [auth BA],
CO [auth BA],
CP [auth BA],
CQ [auth BA],
CR [auth BA],
CS [auth CA],
CT [auth CA],
CU [auth CA],
CV [auth CA],
CW [auth DA],
CX [auth DA],
CY [auth DA],
CZ [auth DA],
DAA [auth DA],
DBA [auth DA],
DCA [auth DA],
DDA [auth DA],
DE [auth AA],
DEA [auth DA],
DF [auth AA],
DFA [auth DA],
DG [auth AA],
DH [auth AX],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth BA],
DM [auth BA],
DN [auth BA],
DO [auth BA],
DP [auth BA],
DQ [auth BA],
DR [auth BA],
DS [auth CA],
DT [auth CA],
DU [auth CA],
DV [auth CA],
DW [auth DA],
DX [auth DA],
DY [auth DA],
DZ [auth DA],
EAA [auth DA],
EBA [auth DA],
ECA [auth DA],
EDA [auth DA],
EE [auth AA],
EEA [auth DA],
EF [auth AA],
EFA [auth DA],
EG [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 BA],
EP [auth BA],
EQ [auth BA],
ER [auth BA],
ES [auth CA],
ET [auth CA],
EU [auth CA],
EV [auth CA],
EW [auth DA],
EX [auth DA],
EY [auth DA],
EZ [auth DA],
FAA [auth DA],
FBA [auth DA],
FCA [auth DA],
FDA [auth DA],
FE [auth AA],
FEA [auth DA],
FF [auth AA],
FFA [auth DA],
FG [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 BA],
FP [auth BA],
FQ [auth BA],
FR [auth BB],
FS [auth CA],
FT [auth CA],
FU [auth CA],
FV [auth CA],
FW [auth DA],
FX [auth DA],
FY [auth DA],
FZ [auth DA],
GAA [auth DA],
GBA [auth DA],
GCA [auth DA],
GDA [auth DA],
GE [auth AA],
GEA [auth DA],
GF [auth AA],
GFA [auth DA],
GG [auth AA],
GH [auth BA],
GI [auth BA],
GJ [auth BA],
GK [auth BA],
GL [auth BA],
GM [auth BA],
GN [auth BA],
GO [auth BA],
GP [auth BA],
GQ [auth BA],
GR [auth BB],
GS [auth CA],
GT [auth CA],
GU [auth CA],
GV [auth CA],
GW [auth DA],
GX [auth DA],
GY [auth DA],
GZ [auth DA],
HAA [auth DA],
HBA [auth DA],
HCA [auth DA],
HDA [auth DA],
HE [auth AA],
HEA [auth DA],
HF [auth AA],
HFA [auth DA],
HG [auth AA],
HH [auth BA],
HI [auth BA],
HJ [auth BA],
HK [auth BA],
HL [auth BA],
HM [auth BA],
HN [auth BA],
HO [auth BA],
HP [auth BA],
HQ [auth BA],
HR [auth BB],
HS [auth CA],
HT [auth CA],
HU [auth CA],
HV [auth CA],
HW [auth DA],
HX [auth DA],
HY [auth DA],
HZ [auth DA],
IAA [auth DA],
IBA [auth DA],
ICA [auth DA],
IDA [auth DA],
IE [auth AA],
IEA [auth DA],
IF [auth AA],
IFA [auth DA],
IG [auth AA],
IH [auth BA],
II [auth BA],
IJ [auth BA],
IK [auth BA],
IL [auth BA],
IM [auth BA],
IN [auth BA],
IO [auth BA],
IP [auth BA],
IQ [auth BA],
IR [auth BB],
IS [auth CA],
IT [auth CA],
IU [auth CA],
IW [auth DA],
IX [auth DA],
IY [auth DA],
IZ [auth DA],
JAA [auth DA],
JBA [auth DA],
JCA [auth DA],
JDA [auth DA],
JE [auth AA],
JEA [auth DA],
JF [auth AA],
JFA [auth DA],
JG [auth AA],
JH [auth BA],
JI [auth BA],
JJ [auth BA],
JK [auth BA],
JL [auth BA],
JM [auth BA],
JN [auth BA],
JO [auth BA],
JP [auth BA],
JQ [auth BA],
JR [auth BE],
JS [auth CA],
JT [auth CA],
JU [auth CA],
JW [auth DA],
JX [auth DA],
JY [auth DA],
JZ [auth DA],
KAA [auth DA],
KBA [auth DA],
KCA [auth DA],
KD [auth AA],
KDA [auth DA],
KE [auth AA],
KEA [auth DA],
KF [auth AA],
KFA [auth DA],
KG [auth AA],
KH [auth BA],
KI [auth BA],
KJ [auth BA],
KK [auth BA],
KL [auth BA],
KM [auth BA],
KN [auth BA],
KO [auth BA],
KP [auth BA],
KQ [auth BA],
KR [auth BF],
KS [auth CA],
KT [auth CA],
KU [auth CA],
KW [auth DA],
KX [auth DA],
KY [auth DA],
KZ [auth DA],
LAA [auth DA],
LBA [auth DA],
LCA [auth DA],
LD [auth AA],
LDA [auth DA],
LE [auth AA],
LEA [auth DA],
LF [auth AA],
LFA [auth DA],
LG [auth AA],
LH [auth BA],
LI [auth BA],
LJ [auth BA],
LK [auth BA],
LL [auth BA],
LM [auth BA],
LN [auth BA],
LO [auth BA],
LP [auth BA],
LQ [auth BA],
LR [auth BF],
LS [auth CA],
LT [auth CA],
LU [auth CA],
LV [auth CV],
LW [auth DA],
LX [auth DA],
LY [auth DA],
LZ [auth DA],
MAA [auth DA],
MBA [auth DA],
MCA [auth DA],
MD [auth AA],
MDA [auth DA],
ME [auth AA],
MEA [auth DA],
MF [auth AA],
MFA [auth DA],
MG [auth AA],
MH [auth BA],
MI [auth BA],
MJ [auth BA],
MK [auth BA],
ML [auth BA],
MM [auth BA],
MN [auth BA],
MO [auth BA],
MP [auth BA],
MQ [auth BA],
MR [auth BO],
MS [auth CA],
MT [auth CA],
MU [auth CA],
MV [auth CV],
MW [auth DA],
MX [auth DA],
MY [auth DA],
MZ [auth DA],
NAA [auth DA],
NBA [auth DA],
NCA [auth DA],
ND [auth AA],
NDA [auth DA],
NE [auth AA],
NEA [auth DA],
NF [auth AA],
NFA [auth DA],
NG [auth AA],
NH [auth BA],
NI [auth BA],
NJ [auth BA],
NK [auth BA],
NL [auth BA],
NM [auth BA],
NN [auth BA],
NO [auth BA],
NP [auth BA],
NQ [auth BA],
NR [auth BU],
NS [auth CA],
NT [auth CA],
NU [auth CA],
NV [auth DA],
NW [auth DA],
NX [auth DA],
NY [auth DA],
NZ [auth DA],
OAA [auth DA],
OBA [auth DA],
OCA [auth DA],
OD [auth AA],
ODA [auth DA],
OE [auth AA],
OEA [auth DA],
OF [auth AA],
OFA [auth DA],
OG [auth AA],
OH [auth BA],
OI [auth BA],
OJ [auth BA],
OK [auth BA],
OL [auth BA],
OM [auth BA],
ON [auth BA],
OO [auth BA],
OP [auth BA],
OQ [auth BA],
OR [auth B1],
OS [auth CA],
OT [auth CA],
OU [auth CA],
OV [auth DA],
OW [auth DA],
OX [auth DA],
OY [auth DA],
OZ [auth DA],
PAA [auth DA],
PBA [auth DA],
PCA [auth DA],
PD [auth AA],
PDA [auth DA],
PE [auth AA],
PEA [auth DA],
PF [auth AA],
PFA [auth DA],
PG [auth AA],
PH [auth BA],
PI [auth BA],
PJ [auth BA],
PK [auth BA],
PL [auth BA],
PM [auth BA],
PN [auth BA],
PO [auth BA],
PP [auth BA],
PQ [auth BA],
PR [auth B3],
PS [auth CA],
PT [auth CA],
PU [auth CA],
PV [auth DA],
PW [auth DA],
PX [auth DA],
PY [auth DA],
PZ [auth DA],
QAA [auth DA],
QBA [auth DA],
QCA [auth DA],
QD [auth AA],
QDA [auth DA],
QE [auth AA],
QEA [auth DA],
QF [auth AA],
QFA [auth DA],
QG [auth AA],
QH [auth BA],
QI [auth BA],
QJ [auth BA],
QK [auth BA],
QL [auth BA],
QM [auth BA],
QN [auth BA],
QO [auth BA],
QP [auth BA],
QQ [auth BA],
QR [auth B5],
QS [auth CA],
QT [auth CA],
QU [auth CA],
QV [auth DA],
QW [auth DA],
QX [auth DA],
QY [auth DA],
QZ [auth DA],
RAA [auth DA],
RBA [auth DA],
RCA [auth DA],
RD [auth AA],
RDA [auth DA],
RE [auth AA],
REA [auth DA],
RF [auth AA],
RFA [auth DA],
RG [auth AA],
RH [auth BA],
RI [auth BA],
RJ [auth BA],
RK [auth BA],
RL [auth BA],
RM [auth BA],
RN [auth BA],
RO [auth BA],
RP [auth BA],
RQ [auth BA],
RR [auth B5],
RS [auth CA],
RT [auth CA],
RU [auth CA],
RV [auth DA],
RW [auth DA],
RX [auth DA],
RY [auth DA],
RZ [auth DA],
SAA [auth DA],
SBA [auth DA],
SCA [auth DA],
SD [auth AA],
SDA [auth DA],
SE [auth AA],
SEA [auth DA],
SF [auth AA],
SFA [auth DA],
SG [auth AA],
SH [auth BA],
SI [auth BA],
SJ [auth BA],
SK [auth BA],
SL [auth BA],
SM [auth BA],
SN [auth BA],
SO [auth BA],
SP [auth BA],
SQ [auth BA],
SR [auth CA],
SS [auth CA],
ST [auth CA],
SU [auth CA],
SV [auth DA],
SW [auth DA],
SX [auth DA],
SY [auth DA],
SZ [auth DA],
TAA [auth DA],
TBA [auth DA],
TCA [auth DA],
TD [auth AA],
TDA [auth DA],
TE [auth AA],
TEA [auth DA],
TF [auth AA],
TFA [auth DA],
TG [auth AA],
TH [auth BA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth BA],
TM [auth BA],
TN [auth BA],
TO [auth BA],
TP [auth BA],
TQ [auth BA],
TR [auth CA],
TS [auth CA],
TT [auth CA],
TU [auth CA],
TV [auth DA],
TW [auth DA],
TX [auth DA],
TY [auth DA],
TZ [auth DA],
UAA [auth DA],
UBA [auth DA],
UCA [auth DA],
UD [auth AA],
UDA [auth DA],
UE [auth AA],
UEA [auth DA],
UF [auth AA],
UFA [auth DA],
UG [auth AA],
UH [auth BA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth BA],
UM [auth BA],
UN [auth BA],
UO [auth BA],
UP [auth BA],
UQ [auth BA],
UR [auth CA],
US [auth CA],
UT [auth CA],
UU [auth CA],
UV [auth DA],
UW [auth DA],
UX [auth DA],
UY [auth DA],
UZ [auth DA],
VAA [auth DA],
VBA [auth DA],
VCA [auth DA],
VD [auth AA],
VDA [auth DA],
VE [auth AA],
VEA [auth DA],
VF [auth AA],
VFA [auth DB],
VG [auth AA],
VH [auth BA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth BA],
VM [auth BA],
VN [auth BA],
VO [auth BA],
VP [auth BA],
VQ [auth BA],
VR [auth CA],
VS [auth CA],
VT [auth CA],
VU [auth CA],
VV [auth DA],
VW [auth DA],
VX [auth DA],
VY [auth DA],
VZ [auth DA],
WAA [auth DA],
WBA [auth DA],
WCA [auth DA],
WD [auth AA],
WDA [auth DA],
WE [auth AA],
WEA [auth DA],
WF [auth AA],
WFA [auth DB],
WG [auth AA],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth BA],
WM [auth BA],
WN [auth BA],
WO [auth BA],
WP [auth BA],
WQ [auth BA],
WR [auth CA],
WS [auth CA],
WT [auth CA],
WU [auth CA],
WV [auth DA],
WW [auth DA],
WX [auth DA],
WY [auth DA],
WZ [auth DA],
XAA [auth DA],
XBA [auth DA],
XCA [auth DA],
XD [auth AA],
XDA [auth DA],
XE [auth AA],
XEA [auth DA],
XF [auth AA],
XFA [auth DD],
XG [auth AA],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XK [auth BA],
XL [auth BA],
XM [auth BA],
XN [auth BA],
XO [auth BA],
XP [auth BA],
XQ [auth BA],
XR [auth CA],
XS [auth CA],
XT [auth CA],
XU [auth CA],
XV [auth DA],
XW [auth DA],
XX [auth DA],
XY [auth DA],
XZ [auth DA],
YAA [auth DA],
YBA [auth DA],
YCA [auth DA],
YD [auth AA],
YDA [auth DA],
YE [auth AA],
YEA [auth DA],
YF [auth AA],
YFA [auth DE],
YG [auth AA],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YK [auth BA],
YL [auth BA],
YM [auth BA],
YN [auth BA],
YO [auth BA],
YP [auth BA],
YQ [auth BA],
YR [auth CA],
YS [auth CA],
YT [auth CA],
YU [auth CA],
YV [auth DA],
YW [auth DA],
YX [auth DA],
YY [auth DA],
YZ [auth DA],
ZAA [auth DA],
ZBA [auth DA],
ZCA [auth DA],
ZD [auth AA],
ZDA [auth DA],
ZE [auth AA],
ZEA [auth DA],
ZF [auth AA],
ZFA [auth D0],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZK [auth BA],
ZL [auth BA],
ZM [auth BA],
ZN [auth BA],
ZO [auth BA],
ZP [auth BA],
ZQ [auth BA],
ZR [auth CA],
ZS [auth CA],
ZT [auth CA],
ZU [auth CA],
ZV [auth DA],
ZW [auth DA],
ZX [auth DA],
ZY [auth DA],
ZZ [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.197α = 90
b = 446.163β = 90
c = 620.953γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXmodel building
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary