4V7P

Recognition of the amber stop codon by release factor RF1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 

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


Literature

Recognition of the amber UAG stop codon by release factor RF1.

Korostelev, A.Zhu, J.Asahara, H.Noller, H.F.

(2010) EMBO J 29: 2577-2585

  • DOI: https://doi.org/10.1038/emboj.2010.139
  • Primary Citation of Related Structures:  
    4V7P

  • PubMed Abstract: 

    We report the crystal structure of a termination complex containing release factor RF1 bound to the 70S ribosome in response to an amber (UAG) codon at 3.6-A resolution. The amber codon is recognized in the 30S subunit-decoding centre directly by conserved elements of domain 2 of RF1, including T186 of the PVT motif. Together with earlier structures, the mechanisms of recognition of all three stop codons by release factors RF1 and RF2 can now be described. Our structure confirms that the backbone amide of Q230 of the universally conserved GGQ motif is positioned to contribute directly to the catalysis of the peptidyl-tRNA hydrolysis reaction through stabilization of the leaving group and/or transition state. We also observe synthetic-negative interactions between mutations in the switch loop of RF1 and in helix 69 of 23S rRNA, revealing that these structural features interact functionally in the termination process. These findings are consistent with our proposal that structural rearrangements of RF1 and RF2 are critical to accurate translation termination.


  • Organizational Affiliation

    Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, UCSC, Santa Cruz, CA, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB],
JC [auth DB]
234Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC],
KC [auth DC]
206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD],
LC [auth DD]
208Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE],
MC [auth DE]
151Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF],
NC [auth DF]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG],
OC [auth DG]
155Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH],
PC [auth DH]
138Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI],
QC [auth DI]
127Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ],
RC [auth DJ]
98Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK],
SC [auth DK]
119Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL],
TC [auth DL]
124Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM],
UC [auth DM]
117Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN],
VC [auth DN]
60Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO],
WC [auth DO]
88Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP],
XC [auth DP]
83Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ],
YC [auth DQ]
99Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR],
ZC [auth DR]
70Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AD [auth DS],
S [auth AS]
78Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BD [auth DT],
T [auth AT]
99Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxCD [auth DU],
U [auth AU]
24Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 1DD [auth DV],
V [auth AV]
354Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth BC],
FB [auth CC]
275Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3BA [auth BD],
GB [auth CD]
206Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth BE],
HB [auth CE]
205Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5DA [auth BF],
IB [auth CF]
181Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6EA [auth BG],
JB [auth CG]
180Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth BH],
KB [auth CH]
148Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10GA [auth BI],
LB [auth CI]
173Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth BJ],
MB [auth CJ]
139Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth BK],
NB [auth CK]
122Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth BL],
OB [auth CL]
150Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16KA [auth BM],
PB [auth CM]
141Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17LA [auth BN],
QB [auth CN]
117Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18MA [auth BO],
RB [auth CO]
111Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19NA [auth BP],
SB [auth CP]
146Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20OA [auth BQ],
TB [auth CQ]
116Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21PA [auth BR],
UB [auth CR]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22QA [auth BS],
VB [auth CS]
112Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23RA [auth BT],
WB [auth CT]
96Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24SA [auth BU],
XB [auth CU]
109Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25TA [auth BV],
YB [auth CV]
206Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27UA [auth BW],
ZB [auth CW]
84Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28AC [auth CX],
VA [auth BX]
98Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29BC [auth CY],
WA [auth BY]
72Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30CC [auth CZ],
XA [auth BZ]
59Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31DC [auth C1],
YA [auth B1]
71Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32EC [auth C2],
ZA [auth B2]
59Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AB [auth B3],
FC [auth C3]
54Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BB [auth B4],
GC [auth C4]
48Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CB [auth B5],
HC [auth C5]
64Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA (1504-MER)A [auth AA],
IC [auth DA]
1,504Thermus thermophilus HB27
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Entity ID: 23
MoleculeChains LengthOrganismImage
P-site tRNA-fMetED [auth DW],
W [auth AW]
77Escherichia coli BL21(DE3)
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Entity ID: 24
MoleculeChains LengthOrganismImage
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')X [auth AX]7Thermus thermophilus HB27
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S ribosomal RNADB [auth CA],
Y [auth BA]
2,879Thermus thermophilus HB27
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S ribosomal RNAEB [auth CB],
Z [auth BB]
119Thermus thermophilus HB27
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Entity ID: 56
MoleculeChains LengthOrganismImage
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')FD [auth DX]9Thermus thermophilus HB27
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BT [auth DD],
CT [auth DN],
SF [auth AD],
TF [auth AN]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AA]
AF [auth AA]
AG [auth BA]
AH [auth BA]
AI [auth BA]
AE [auth AA],
AF [auth AA],
AG [auth BA],
AH [auth BA],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AL [auth BA],
AM [auth BA],
AN [auth CA],
AO [auth CA],
AP [auth CA],
AQ [auth CA],
AR [auth CA],
AS [auth DA],
AT [auth DA],
BE [auth AA],
BF [auth AA],
BG [auth BA],
BH [auth BA],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth BA],
BM [auth BA],
BN [auth CA],
BO [auth CA],
BP [auth CA],
BQ [auth CA],
BR [auth CA],
BS [auth DA],
CE [auth AA],
CF [auth AA],
CG [auth BA],
CH [auth BA],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth BA],
CM [auth BA],
CN [auth CA],
CO [auth CA],
CP [auth CA],
CQ [auth CA],
CR [auth CA],
CS [auth DA],
DE [auth AA],
DF [auth AA],
DG [auth BA],
DH [auth BA],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth BA],
DM [auth BA],
DN [auth CA],
DO [auth CA],
DP [auth CA],
DQ [auth CA],
DR [auth CA],
DS [auth DA],
DT [auth DW],
EE [auth AA],
EF [auth AA],
EG [auth BA],
EH [auth BA],
EI [auth BA],
EJ [auth BA],
EK [auth BA],
EL [auth BA],
EM [auth BA],
EN [auth CA],
EO [auth CA],
EP [auth CA],
EQ [auth CA],
ER [auth CA],
ES [auth DA],
FE [auth AA],
FF [auth AA],
FG [auth BA],
FH [auth BA],
FI [auth BA],
FJ [auth BA],
FK [auth BA],
FL [auth BA],
FM [auth BA],
FN [auth CA],
FO [auth CA],
FP [auth CA],
FQ [auth CA],
FR [auth CA],
FS [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 CA],
GO [auth CA],
GP [auth CA],
GQ [auth CA],
GR [auth CA],
GS [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 CA],
HO [auth CA],
HP [auth CA],
HQ [auth CA],
HR [auth CA],
HS [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 CA],
IO [auth CA],
IP [auth CA],
IQ [auth CA],
IR [auth CA],
IS [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 CA],
JO [auth CA],
JP [auth CA],
JQ [auth CA],
JR [auth CA],
JS [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 CA],
KO [auth CA],
KP [auth CA],
KQ [auth CA],
KR [auth CA],
KS [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 CA],
LO [auth CA],
LP [auth CA],
LQ [auth CA],
LR [auth CA],
LS [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 CA],
MO [auth CA],
MP [auth CA],
MQ [auth CA],
MR [auth CA],
MS [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 CA],
NO [auth CA],
NP [auth CA],
NQ [auth CA],
NR [auth CA],
NS [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 CA],
OO [auth CA],
OP [auth CA],
OQ [auth CA],
OR [auth CA],
OS [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 CA],
PO [auth CA],
PP [auth CA],
PQ [auth CA],
PR [auth CA],
PS [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 CA],
QO [auth CA],
QP [auth CA],
QQ [auth CA],
QR [auth CA],
QS [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 CA],
RO [auth CA],
RP [auth CA],
RQ [auth CA],
RR [auth CA],
RS [auth DA],
SD [auth AA],
SE [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 CA],
SO [auth CA],
SP [auth CA],
SQ [auth CA],
SR [auth CA],
SS [auth DA],
TD [auth AA],
TE [auth AA],
TG [auth BA],
TH [auth BA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth BA],
TM [auth BB],
TN [auth CA],
TO [auth CA],
TP [auth CA],
TQ [auth CA],
TR [auth CB],
TS [auth DA],
UD [auth AA],
UE [auth AA],
UF [auth AT],
UG [auth BA],
UH [auth BA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth BA],
UM [auth BB],
UN [auth CA],
UO [auth CA],
UP [auth CA],
UQ [auth CA],
UR [auth CB],
US [auth DA],
VD [auth AA],
VE [auth AA],
VF [auth AV],
VG [auth BA],
VH [auth BA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth BA],
VM [auth BK],
VN [auth CA],
VO [auth CA],
VP [auth CA],
VQ [auth CA],
VR [auth CM],
VS [auth DA],
WD [auth AA],
WE [auth AA],
WF [auth AW],
WG [auth BA],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth BA],
WM [auth BM],
WN [auth CA],
WO [auth CA],
WP [auth CA],
WQ [auth CA],
WR [auth CY],
WS [auth DA],
XD [auth AA],
XE [auth AA],
XF [auth AW],
XG [auth BA],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XK [auth BA],
XL [auth BA],
XM [auth B2],
XN [auth CA],
XO [auth CA],
XP [auth CA],
XQ [auth CA],
XR [auth DA],
XS [auth DA],
YD [auth AA],
YE [auth AA],
YF [auth AW],
YG [auth BA],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YK [auth BA],
YL [auth BA],
YM [auth CA],
YN [auth CA],
YO [auth CA],
YP [auth CA],
YQ [auth CA],
YR [auth DA],
YS [auth DA],
ZD [auth AA],
ZE [auth AA],
ZF [auth BA],
ZG [auth BA],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZK [auth BA],
ZL [auth BA],
ZM [auth CA],
ZN [auth CA],
ZO [auth CA],
ZP [auth CA],
ZQ [auth CA],
ZR [auth DA],
ZS [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.38α = 90
b = 452.7β = 90
c = 617.09γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSrefinement
XDSdata reduction
CNSphasing

Structure Validation

View Full Validation Report



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