4V8X

Structure of Thermus thermophilus ribosome

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Yoeb-Ribosome Structure: A Canonical Rnase that Requires the Ribosome for its Specific Activity.

Feng, S., Chen, Y., Kamada, K., Wang, H., Tang, K., Wang, M., Gao, Y.

(2013) Nucleic Acids Res 41: 9549

  • DOI: https://doi.org/10.1093/nar/gkt742
  • Primary Citation of Related Structures:  
    4V8X

  • PubMed Abstract: 

    As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3'-phosphate at the newly formed 3' end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity.

    • Organizational Affiliation: 

    School of Biological Science, Nanyang Technological University, 637551 Singapore, RIKEN Advanced Science Institute, Saitama 351-0198, Japan, Swiss Light Source, Paul Scherrer Institut, CH-5232, Switzerland and Institute of Molecular and Cell Biology, A-STAR, 138673, Singapore.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B [auth AB],
IB [auth CB]		256Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C [auth AC],
JB [auth CC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D [auth AD],
KB [auth CD]		209Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E [auth AE],
LB [auth CE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F [auth AF],
MB [auth CF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G [auth AG],
NB [auth CG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H [auth AH],
OB [auth CH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I [auth AI],
PB [auth CI]		128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J [auth AJ],
QB [auth CJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K [auth AK],
RB [auth CK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L [auth AL],
SB [auth CL]		132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M [auth AM],
TB [auth CM]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14 TYPE ZN [auth AN],
UB [auth CN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O [auth AO],
VB [auth CO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P [auth AP],
WB [auth CP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q [auth AQ],
XB [auth CQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R [auth AR],
YB [auth CR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S [auth AS],
ZB [auth CS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20AC [auth CT],
T [auth AT]		106Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXBC [auth CU],
U [auth AU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEMFC [auth CY],
GC [auth CZ],
Y [auth AY],
Z [auth AZ]		84Escherichia coli K-12Mutation(s): 0 
Gene Names: B1563, JW1555, RELE
EC: 3.1
UniProt
Find proteins for P69348 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27AA [auth B0],
HC [auth D0]		85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28BA [auth B1],
IC [auth D1]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29CA [auth B2],
JC [auth D2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30DA [auth B3],
KC [auth D3]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31EA [auth B4],
LC [auth D4]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32FA [auth B5],
MC [auth D5]		60Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33GA [auth B6],
NC [auth D6]		54Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34HA [auth B7],
OC [auth D7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35IA [auth B8],
PC [auth D8]		65Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36JA [auth B9],
QC [auth D9]		37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1MA [auth BC],
TC [auth DC]		229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2NA [auth BD],
UC [auth DD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3OA [auth BE],
VC [auth DE]		206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4PA [auth BF],
WC [auth DF]		210Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5QA [auth BG],
XC [auth DG]		182Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6RA [auth BH],
YC [auth DH]		180Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L9SA [auth BI],
ZC [auth DI]		148Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10AD [auth DJ],
TA [auth BJ]		130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13BD [auth DN],
UA [auth BN]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14CD [auth DO],
VA [auth BO]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15DD [auth DP],
WA [auth BP]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16ED [auth DQ],
XA [auth BQ]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17FD [auth DR],
YA [auth BR]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18GD [auth DS],
ZA [auth BS]		112Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19AB [auth BT],
HD [auth DT]		146Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20BB [auth BU],
ID [auth DU]		118Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21CB [auth BV],
JD [auth DV]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22DB [auth BW],
KD [auth DW]		113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23EB [auth BX],
LD [auth DX]		96Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24FB [auth BY],
MD [auth DY]		110Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25GB [auth BZ],
ND [auth DZ]		206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA],
HB [auth CA]		1,504Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
transfer RNAV [auth AV]77Thermus thermophilus HB8
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Entity ID: 23
MoleculeChains LengthOrganismImage
transfer RNACC [auth CV],
DC [auth CW],
W [auth AW]		77Thermus thermophilus HB8
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Entity ID: 24
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*AP*AP*AP *AP*AP*UP*G U2M A2M A2MP*AP*AP*AP*A)-3'X [auth AX]25synthetic construct
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Entity ID: 36
MoleculeChains LengthOrganismImage
23S ribosomal RNAKA [auth BA],
RC [auth DA]		2,848Thermus thermophilus HB8
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Entity ID: 37
MoleculeChains LengthOrganismImage
5S ribosomal RNALA [auth BB],
SC [auth DB]		119Thermus thermophilus HB8
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Entity ID: 59
MoleculeChains LengthOrganismImage
BACTERIAL TOXIN YOEBEC [auth CX]10Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
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DV [auth CD],
GV [auth CN],
NH [auth AD],
PH [auth AN]		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],
AG [auth AA],
AH [auth AA],
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 BB],
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],
BG [auth AA],
BH [auth AA],
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 BF],
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],
CG [auth AA],
CH [auth AA],
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 BP],
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],
DG [auth AA],
DH [auth AA],
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 BX],
DS [auth CA],
DT [auth CA],
DU [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],
EG [auth AA],
EH [auth AA],
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 CA],
ES [auth CA],
ET [auth CA],
EU [auth CA],
EV [auth CG],
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],
FG [auth AA],
FH [auth AA],
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 CA],
FS [auth CA],
FT [auth CA],
FU [auth CA],
FV [auth CL],
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],
GG [auth AA],
GH [auth AA],
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 CA],
GS [auth CA],
GT [auth CA],
GU [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],
HG [auth AA],
HH [auth AA],
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 CA],
HS [auth CA],
HT [auth CA],
HU [auth CA],
HV [auth CV],
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],
IG [auth AA],
IH [auth AA],
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 CA],
IS [auth CA],
IT [auth CA],
IU [auth CA],
IV [auth CV],
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],
JG [auth AA],
JH [auth AA],
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 CA],
JS [auth CA],
JT [auth CA],
JU [auth CA],
JV [auth D1],
JW [auth DA],
JX [auth DA],
JY [auth DA],
JZ [auth DA],
KAA [auth DA],
KBA [auth DA],
KCA [auth DA],
KDA [auth DA],
KE [auth AA],
KEA [auth DA],
KF [auth AA],
KG [auth AA],
KH [auth AA],
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 CA],
KS [auth CA],
KT [auth CA],
KU [auth CA],
KV [auth D5],
KW [auth DA],
KX [auth DA],
KY [auth DA],
KZ [auth DA],
LAA [auth DA],
LBA [auth DA],
LCA [auth DA],
LDA [auth DA],
LE [auth AA],
LEA [auth DA],
LF [auth AA],
LG [auth AA],
LH [auth AA],
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 CA],
LS [auth CA],
LT [auth CA],
LU [auth CA],
LV [auth DA],
LW [auth DA],
LX [auth DA],
LY [auth DA],
LZ [auth DA],
MAA [auth DA],
MBA [auth DA],
MCA [auth DA],
MDA [auth DA],
ME [auth AA],
MEA [auth DA],
MF [auth AA],
MG [auth AA],
MH [auth AA],
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 CA],
MS [auth CA],
MT [auth CA],
MU [auth CA],
MV [auth DA],
MW [auth DA],
MX [auth DA],
MY [auth DA],
MZ [auth DA],
NAA [auth DA],
NBA [auth DA],
NCA [auth DA],
NDA [auth DA],
NE [auth AA],
NEA [auth DA],
NF [auth AA],
NG [auth AA],
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 CA],
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],
OG [auth AA],
OH [auth AL],
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 CA],
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],
PG [auth AA],
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 CA],
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],
QG [auth AA],
QH [auth AV],
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 CA],
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],
RG [auth AA],
RH [auth AX],
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 CA],
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],
SG [auth AA],
SH [auth B0],
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 DB],
TF [auth AA],
TG [auth AA],
TH [auth B1],
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 DF],
UF [auth AA],
UG [auth AA],
UH [auth B1],
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 DR],
VF [auth AA],
VG [auth AA],
VH [auth B5],
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 DX],
WF [auth AA],
WG [auth AA],
WH [auth B5],
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],
XF [auth AA],
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],
YF [auth AA],
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],
ZF [auth AA],
ZG [auth AA],
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 BB],
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: 3.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.594α = 90
b = 455.434β = 90
c = 616.94γ = 90
Software Package:
Software NamePurpose
CNSmodel building
CNSrefinement
CNSdata reduction
CNSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



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: 2016-07-27
    Changes: Derived calculations
  • Version 1.3: 2018-04-04
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description