8FOM

Crystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis for reduced ribosomal A-site fidelity in response to P-site codon-anticodon mismatches.

Nguyen, H.A., Hoffer, E.D., Fagan, C.E., Maehigashi, T., Dunham, C.M.

(2023) J Biol Chem 299: 104608-104608

  • DOI: https://doi.org/10.1016/j.jbc.2023.104608
  • Primary Citation of Related Structures:  
    8FOM, 8FON

  • PubMed Abstract: 

    Rapid and accurate translation is essential in all organisms to produce properly folded and functional proteins. mRNA codons that define the protein-coding sequences are decoded by tRNAs on the ribosome in the aminoacyl (A) binding site. The mRNA codon and the tRNA anticodon interaction is extensively monitored by the ribosome to ensure accuracy in tRNA selection. While other polymerases that synthesize DNA and RNA can correct for misincorporations, the ribosome is unable to correct mistakes. Instead, when a misincorporation occurs, the mismatched tRNA-mRNA pair moves to the peptidyl (P) site and, from this location, causes a reduction in the fidelity at the A site, triggering post-peptidyl transfer quality control. This reduced fidelity allows for additional incorrect tRNAs to be accepted and for release factor 2 (RF2) to recognize sense codons, leading to hydrolysis of the aberrant peptide. Here, we present crystal structures of the ribosome containing a tRNA Lys in the P site with a U•U mismatch with the mRNA codon. We find that when the mismatch occurs in the second position of the P-site codon-anticodon interaction, the first nucleotide of the A-site codon flips from the mRNA path to engage highly conserved 16S rRNA nucleotide A1493 in the decoding center. We propose that this mRNA nucleotide mispositioning leads to reduced fidelity at the A site. Further, this state may provide an opportunity for RF2 to initiate premature termination before erroneous nascent chains disrupt the cellular proteome.

    • Organizational Affiliation: 

    Department of Chemistry, Emory University, Atlanta, Georgia, USA; Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, Georgia, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth QB],
DB [auth XB]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth QC],
EB [auth XC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth QD],
FB [auth XD]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth QE],
GB [auth XE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth QF],
HB [auth XF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth QG],
IB [auth XG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth QH],
JB [auth XH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth QI],
KB [auth XI]		128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth QJ],
LB [auth XJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth QK],
MB [auth XK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth QL],
NB [auth XL]		131Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth QM],
OB [auth XM]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth QN],
PB [auth XN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth QO],
QB [auth XO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth QP],
RB [auth XP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth QQ],
SB [auth XQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth QR],
TB [auth XR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth QS],
UB [auth XS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth QT],
VB [auth XT]		106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth QU],
WB [auth XU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AC [auth Y0],
X [auth R0]		85Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BC [auth Y1],
Y [auth R1]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CC [auth Y2],
Z [auth R2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth R3],
DC [auth Y3]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31BA [auth R4],
EC [auth Y4]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth R5],
FC [auth Y5]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33DA [auth R6],
GC [auth Y6]		54Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth R7],
HC [auth Y7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth R8],
IC [auth Y8]		65Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth R9],
JC [auth Y9]		37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2JA [auth RD],
MC [auth YD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3KA [auth RE],
NC [auth YE]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4LA [auth RF],
OC [auth YF]		210Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5MA [auth RG],
PC [auth YG]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6NA [auth RH],
QC [auth YH]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9OA [auth RI],
RC [auth YI]		148Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PA [auth RN],
SC [auth YN]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14QA [auth RO],
TC [auth YO]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15RA [auth RP],
UC [auth YP]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16SA [auth RQ],
VC [auth YQ]		141Thermus thermophilus HB8Mutation(s): 0 
UniProt
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UniProt GroupP60489
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17TA [auth RR],
WC [auth YR]		118Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ9Z9H5
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18UA [auth RS],
XC [auth YS]		112Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19VA [auth RT],
YC [auth YT]		146Thermus thermophilus HB8Mutation(s): 0 
UniProt
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UniProt GroupP60490
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20WA [auth RU],
ZC [auth YU]		118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupP60491
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21AD [auth YV],
XA [auth RV]		101Thermus thermophilus HB8Mutation(s): 0 
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UniProt GroupP60492
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22BD [auth YW],
YA [auth RW]		113Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23CD [auth YX],
ZA [auth RX]		96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24AB [auth RY],
DD [auth YY]		110Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25BB [auth RZ],
ED [auth YZ]		206Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth QA],
CB [auth XA]		1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-site tRNA^Lys(SUU)V [auth QV],
XB [auth XV]		76Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
mRNAW [auth QX],
YB [auth XX]		23Escherichia coli
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Entity ID: 34
MoleculeChains LengthOrganismImage
23S rRNAHA [auth RA],
KC [auth YA]		2,915Thermus thermophilus HB8
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Entity ID: 35
MoleculeChains LengthOrganismImage
5S rRNAIA [auth RB],
LC [auth YB]		122Thermus thermophilus HB8
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Entity ID: 55
MoleculeChains LengthOrganismImage
A-site ASL^PheZB [auth XY]17Escherichia coli
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Entity ID: 56
MoleculeChains LengthOrganismImage
CC-puroFD [auth Z6],
GD [auth Z8]		3synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
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AV [auth XD],
JF [auth QD]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN
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BV [auth XN],
KF [auth QN]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AAA [auth YA]
ABA [auth YA]
ACA [auth YA]
ADA [auth YA]
AE [auth QA]
AAA [auth YA],
ABA [auth YA],
ACA [auth YA],
ADA [auth YA],
AE [auth QA],
AEA [auth YA],
AF [auth QA],
AFA [auth YA],
AG [auth RA],
AGA [auth YA],
AH [auth RA],
AHA [auth YA],
AI [auth RA],
AIA [auth YA],
AJ [auth RA],
AJA [auth YA],
AK [auth RA],
AL [auth RA],
AM [auth RA],
AN [auth RA],
AO [auth RA],
AP [auth RA],
AQ [auth RA],
AR [auth RA],
AS [auth RA],
AT [auth XA],
AU [auth XA],
AW [auth YA],
AX [auth YA],
AY [auth YA],
AZ [auth YA],
BAA [auth YA],
BBA [auth YA],
BCA [auth YA],
BDA [auth YA],
BE [auth QA],
BEA [auth YA],
BF [auth QA],
BFA [auth YA],
BG [auth RA],
BGA [auth YA],
BH [auth RA],
BHA [auth YA],
BI [auth RA],
BIA [auth YA],
BJ [auth RA],
BJA [auth YA],
BK [auth RA],
BL [auth RA],
BM [auth RA],
BN [auth RA],
BO [auth RA],
BP [auth RA],
BQ [auth RA],
BR [auth RA],
BS [auth RA],
BT [auth XA],
BU [auth XA],
BW [auth YA],
BX [auth YA],
BY [auth YA],
BZ [auth YA],
CAA [auth YA],
CBA [auth YA],
CCA [auth YA],
CDA [auth YA],
CE [auth QA],
CEA [auth YA],
CF [auth QA],
CFA [auth YA],
CG [auth RA],
CGA [auth YA],
CH [auth RA],
CHA [auth YA],
CI [auth RA],
CIA [auth YA],
CJ [auth RA],
CJA [auth YA],
CK [auth RA],
CL [auth RA],
CM [auth RA],
CN [auth RA],
CO [auth RA],
CP [auth RA],
CQ [auth RA],
CR [auth RA],
CS [auth RA],
CT [auth XA],
CU [auth XA],
CV [auth XV],
CW [auth YA],
CX [auth YA],
CY [auth YA],
CZ [auth YA],
DAA [auth YA],
DBA [auth YA],
DCA [auth YA],
DDA [auth YA],
DE [auth QA],
DEA [auth YA],
DF [auth QA],
DFA [auth YA],
DG [auth RA],
DGA [auth YA],
DH [auth RA],
DHA [auth YA],
DI [auth RA],
DIA [auth YA],
DJ [auth RA],
DJA [auth YA],
DK [auth RA],
DL [auth RA],
DM [auth RA],
DN [auth RA],
DO [auth RA],
DP [auth RA],
DQ [auth RA],
DR [auth RA],
DS [auth RA],
DT [auth XA],
DU [auth XA],
DV [auth XV],
DW [auth YA],
DX [auth YA],
DY [auth YA],
DZ [auth YA],
EAA [auth YA],
EBA [auth YA],
ECA [auth YA],
EDA [auth YA],
EE [auth QA],
EEA [auth YA],
EF [auth QA],
EFA [auth YA],
EG [auth RA],
EGA [auth YA],
EH [auth RA],
EHA [auth YA],
EI [auth RA],
EIA [auth YA],
EJ [auth RA],
EJA [auth YA],
EK [auth RA],
EL [auth RA],
EM [auth RA],
EN [auth RA],
EO [auth RA],
EP [auth RA],
EQ [auth RA],
ER [auth RA],
ES [auth RA],
ET [auth XA],
EU [auth XA],
EV [auth XX],
EW [auth YA],
EX [auth YA],
EY [auth YA],
EZ [auth YA],
FAA [auth YA],
FBA [auth YA],
FCA [auth YA],
FDA [auth YA],
FE [auth QA],
FEA [auth YA],
FF [auth QA],
FFA [auth YA],
FG [auth RA],
FGA [auth YA],
FH [auth RA],
FHA [auth YA],
FI [auth RA],
FIA [auth YA],
FJ [auth RA],
FJA [auth YA],
FK [auth RA],
FL [auth RA],
FM [auth RA],
FN [auth RA],
FO [auth RA],
FP [auth RA],
FQ [auth RA],
FR [auth RA],
FS [auth RA],
FT [auth XA],
FU [auth XA],
FV [auth Y0],
FW [auth YA],
FX [auth YA],
FY [auth YA],
FZ [auth YA],
GAA [auth YA],
GBA [auth YA],
GCA [auth YA],
GDA [auth YA],
GE [auth QA],
GEA [auth YA],
GF [auth QA],
GFA [auth YA],
GG [auth RA],
GGA [auth YA],
GH [auth RA],
GHA [auth YA],
GI [auth RA],
GIA [auth YA],
GJ [auth RA],
GJA [auth YA],
GK [auth RA],
GL [auth RA],
GM [auth RA],
GN [auth RA],
GO [auth RA],
GP [auth RA],
GQ [auth RA],
GR [auth RA],
GS [auth RA],
GT [auth XA],
GU [auth XA],
GV [auth Y1],
GW [auth YA],
GX [auth YA],
GY [auth YA],
GZ [auth YA],
HAA [auth YA],
HBA [auth YA],
HCA [auth YA],
HD [auth QA],
HDA [auth YA],
HE [auth QA],
HEA [auth YA],
HF [auth QA],
HFA [auth YA],
HG [auth RA],
HGA [auth YA],
HH [auth RA],
HHA [auth YA],
HI [auth RA],
HIA [auth YA],
HJ [auth RA],
HJA [auth YA],
HK [auth RA],
HL [auth RA],
HM [auth RA],
HN [auth RA],
HO [auth RA],
HP [auth RA],
HQ [auth RA],
HR [auth RA],
HS [auth RA],
HT [auth XA],
HU [auth XA],
HV [auth Y3],
HW [auth YA],
HX [auth YA],
HY [auth YA],
HZ [auth YA],
IAA [auth YA],
IBA [auth YA],
ICA [auth YA],
ID [auth QA],
IDA [auth YA],
IE [auth QA],
IEA [auth YA],
IF [auth QA],
IFA [auth YA],
IG [auth RA],
IGA [auth YA],
IH [auth RA],
IHA [auth YA],
II [auth RA],
IIA [auth YA],
IJ [auth RA],
IJA [auth YB],
IK [auth RA],
IL [auth RA],
IM [auth RA],
IN [auth RA],
IO [auth RA],
IP [auth RA],
IQ [auth RA],
IR [auth RA],
IS [auth RA],
IT [auth XA],
IU [auth XA],
IV [auth Y5],
IW [auth YA],
IX [auth YA],
IY [auth YA],
IZ [auth YA],
JAA [auth YA],
JBA [auth YA],
JCA [auth YA],
JD [auth QA],
JDA [auth YA],
JE [auth QA],
JEA [auth YA],
JFA [auth YA],
JG [auth RA],
JGA [auth YA],
JH [auth RA],
JHA [auth YA],
JI [auth RA],
JIA [auth YA],
JJ [auth RA],
JJA [auth YB],
JK [auth RA],
JL [auth RA],
JM [auth RA],
JN [auth RA],
JO [auth RA],
JP [auth RA],
JQ [auth RA],
JR [auth RA],
JS [auth RA],
JT [auth XA],
JU [auth XA],
JV [auth Y7],
JW [auth YA],
JX [auth YA],
JY [auth YA],
JZ [auth YA],
KAA [auth YA],
KBA [auth YA],
KCA [auth YA],
KD [auth QA],
KDA [auth YA],
KE [auth QA],
KEA [auth YA],
KFA [auth YA],
KG [auth RA],
KGA [auth YA],
KH [auth RA],
KHA [auth YA],
KI [auth RA],
KIA [auth YA],
KJ [auth RA],
KJA [auth YB],
KK [auth RA],
KL [auth RA],
KM [auth RA],
KN [auth RA],
KO [auth RA],
KP [auth RA],
KQ [auth RA],
KR [auth RA],
KS [auth RA],
KT [auth XA],
KU [auth XA],
KV [auth Y7],
KW [auth YA],
KX [auth YA],
KY [auth YA],
KZ [auth YA],
LAA [auth YA],
LBA [auth YA],
LCA [auth YA],
LD [auth QA],
LDA [auth YA],
LE [auth QA],
LEA [auth YA],
LF [auth QV],
LFA [auth YA],
LG [auth RA],
LGA [auth YA],
LH [auth RA],
LHA [auth YA],
LI [auth RA],
LIA [auth YA],
LJ [auth RA],
LJA [auth YB],
LK [auth RA],
LL [auth RA],
LM [auth RA],
LN [auth RA],
LO [auth RA],
LP [auth RA],
LQ [auth RA],
LR [auth RA],
LS [auth RB],
LT [auth XA],
LU [auth XA],
LV [auth YA],
LW [auth YA],
LX [auth YA],
LY [auth YA],
LZ [auth YA],
MAA [auth YA],
MBA [auth YA],
MCA [auth YA],
MD [auth QA],
MDA [auth YA],
ME [auth QA],
MEA [auth YA],
MF [auth R0],
MFA [auth YA],
MG [auth RA],
MGA [auth YA],
MH [auth RA],
MHA [auth YA],
MI [auth RA],
MIA [auth YA],
MJ [auth RA],
MJA [auth YE],
MK [auth RA],
ML [auth RA],
MM [auth RA],
MN [auth RA],
MO [auth RA],
MP [auth RA],
MQ [auth RA],
MR [auth RA],
MS [auth RB],
MT [auth XA],
MU [auth XA],
MV [auth YA],
MW [auth YA],
MX [auth YA],
MY [auth YA],
MZ [auth YA],
NAA [auth YA],
NBA [auth YA],
NCA [auth YA],
ND [auth QA],
NDA [auth YA],
NE [auth QA],
NEA [auth YA],
NF [auth R5],
NFA [auth YA],
NG [auth RA],
NGA [auth YA],
NH [auth RA],
NHA [auth YA],
NI [auth RA],
NIA [auth YA],
NJ [auth RA],
NJA [auth YE],
NK [auth RA],
NL [auth RA],
NM [auth RA],
NN [auth RA],
NO [auth RA],
NP [auth RA],
NQ [auth RA],
NR [auth RA],
NS [auth RB],
NT [auth XA],
NU [auth XA],
NV [auth YA],
NW [auth YA],
NX [auth YA],
NY [auth YA],
NZ [auth YA],
OAA [auth YA],
OBA [auth YA],
OCA [auth YA],
OD [auth QA],
ODA [auth YA],
OE [auth QA],
OEA [auth YA],
OF [auth R7],
OFA [auth YA],
OG [auth RA],
OGA [auth YA],
OH [auth RA],
OHA [auth YA],
OI [auth RA],
OIA [auth YA],
OJ [auth RA],
OJA [auth YP],
OK [auth RA],
OL [auth RA],
OM [auth RA],
ON [auth RA],
OO [auth RA],
OP [auth RA],
OQ [auth RA],
OR [auth RA],
OS [auth RB],
OT [auth XA],
OU [auth XA],
OV [auth YA],
OW [auth YA],
OX [auth YA],
OY [auth YA],
OZ [auth YA],
PAA [auth YA],
PBA [auth YA],
PCA [auth YA],
PD [auth QA],
PDA [auth YA],
PE [auth QA],
PEA [auth YA],
PF [auth R8],
PFA [auth YA],
PG [auth RA],
PGA [auth YA],
PH [auth RA],
PHA [auth YA],
PI [auth RA],
PIA [auth YA],
PJ [auth RA],
PJA [auth YP],
PK [auth RA],
PL [auth RA],
PM [auth RA],
PN [auth RA],
PO [auth RA],
PP [auth RA],
PQ [auth RA],
PR [auth RA],
PS [auth RB],
PT [auth XA],
PU [auth XA],
PV [auth YA],
PW [auth YA],
PX [auth YA],
PY [auth YA],
PZ [auth YA],
QAA [auth YA],
QBA [auth YA],
QCA [auth YA],
QD [auth QA],
QDA [auth YA],
QE [auth QA],
QEA [auth YA],
QF [auth RA],
QFA [auth YA],
QG [auth RA],
QGA [auth YA],
QH [auth RA],
QHA [auth YA],
QI [auth RA],
QIA [auth YA],
QJ [auth RA],
QJA [auth YQ],
QK [auth RA],
QL [auth RA],
QM [auth RA],
QN [auth RA],
QO [auth RA],
QP [auth RA],
QQ [auth RA],
QR [auth RA],
QS [auth RE],
QT [auth XA],
QU [auth XA],
QV [auth YA],
QW [auth YA],
QX [auth YA],
QY [auth YA],
QZ [auth YA],
RAA [auth YA],
RBA [auth YA],
RCA [auth YA],
RD [auth QA],
RDA [auth YA],
RE [auth QA],
REA [auth YA],
RF [auth RA],
RFA [auth YA],
RG [auth RA],
RGA [auth YA],
RH [auth RA],
RHA [auth YA],
RI [auth RA],
RIA [auth YA],
RJ [auth RA],
RJA [auth YQ],
RK [auth RA],
RL [auth RA],
RM [auth RA],
RN [auth RA],
RO [auth RA],
RP [auth RA],
RQ [auth RA],
RR [auth RA],
RS [auth RF],
RT [auth XA],
RU [auth XA],
RV [auth YA],
RW [auth YA],
RX [auth YA],
RY [auth YA],
RZ [auth YA],
SAA [auth YA],
SBA [auth YA],
SCA [auth YA],
SD [auth QA],
SDA [auth YA],
SE [auth QA],
SEA [auth YA],
SF [auth RA],
SFA [auth YA],
SG [auth RA],
SGA [auth YA],
SH [auth RA],
SHA [auth YA],
SI [auth RA],
SIA [auth YA],
SJ [auth RA],
SJA [auth YR],
SK [auth RA],
SL [auth RA],
SM [auth RA],
SN [auth RA],
SO [auth RA],
SP [auth RA],
SQ [auth RA],
SR [auth RA],
SS [auth RR],
ST [auth XA],
SU [auth XA],
SV [auth YA],
SW [auth YA],
SX [auth YA],
SY [auth YA],
SZ [auth YA],
TAA [auth YA],
TBA [auth YA],
TCA [auth YA],
TD [auth QA],
TDA [auth YA],
TE [auth QA],
TEA [auth YA],
TF [auth RA],
TFA [auth YA],
TG [auth RA],
TGA [auth YA],
TH [auth RA],
THA [auth YA],
TI [auth RA],
TIA [auth YA],
TJ [auth RA],
TJA [auth YR],
TK [auth RA],
TL [auth RA],
TM [auth RA],
TN [auth RA],
TO [auth RA],
TP [auth RA],
TQ [auth RA],
TR [auth RA],
TS [auth RR],
TT [auth XA],
TU [auth XA],
TV [auth YA],
TW [auth YA],
TX [auth YA],
TY [auth YA],
TZ [auth YA],
UAA [auth YA],
UBA [auth YA],
UCA [auth YA],
UD [auth QA],
UDA [auth YA],
UE [auth QA],
UEA [auth YA],
UF [auth RA],
UFA [auth YA],
UG [auth RA],
UGA [auth YA],
UH [auth RA],
UHA [auth YA],
UI [auth RA],
UIA [auth YA],
UJ [auth RA],
UJA [auth YY],
UK [auth RA],
UL [auth RA],
UM [auth RA],
UN [auth RA],
UO [auth RA],
UP [auth RA],
UQ [auth RA],
UR [auth RA],
US [auth XA],
UT [auth XA],
UU [auth XA],
UV [auth YA],
UW [auth YA],
UX [auth YA],
UY [auth YA],
UZ [auth YA],
VAA [auth YA],
VBA [auth YA],
VCA [auth YA],
VD [auth QA],
VDA [auth YA],
VE [auth QA],
VEA [auth YA],
VF [auth RA],
VFA [auth YA],
VG [auth RA],
VGA [auth YA],
VH [auth RA],
VHA [auth YA],
VI [auth RA],
VIA [auth YA],
VJ [auth RA],
VK [auth RA],
VL [auth RA],
VM [auth RA],
VN [auth RA],
VO [auth RA],
VP [auth RA],
VQ [auth RA],
VR [auth RA],
VS [auth XA],
VT [auth XA],
VU [auth XA],
VV [auth YA],
VW [auth YA],
VX [auth YA],
VY [auth YA],
VZ [auth YA],
WAA [auth YA],
WBA [auth YA],
WCA [auth YA],
WD [auth QA],
WDA [auth YA],
WE [auth QA],
WEA [auth YA],
WF [auth RA],
WFA [auth YA],
WG [auth RA],
WGA [auth YA],
WH [auth RA],
WHA [auth YA],
WI [auth RA],
WIA [auth YA],
WJ [auth RA],
WK [auth RA],
WL [auth RA],
WM [auth RA],
WN [auth RA],
WO [auth RA],
WP [auth RA],
WQ [auth RA],
WR [auth RA],
WS [auth XA],
WT [auth XA],
WU [auth XA],
WV [auth YA],
WW [auth YA],
WX [auth YA],
WY [auth YA],
WZ [auth YA],
XAA [auth YA],
XBA [auth YA],
XCA [auth YA],
XD [auth QA],
XDA [auth YA],
XE [auth QA],
XEA [auth YA],
XF [auth RA],
XFA [auth YA],
XG [auth RA],
XGA [auth YA],
XH [auth RA],
XHA [auth YA],
XI [auth RA],
XIA [auth YA],
XJ [auth RA],
XK [auth RA],
XL [auth RA],
XM [auth RA],
XN [auth RA],
XO [auth RA],
XP [auth RA],
XQ [auth RA],
XR [auth RA],
XS [auth XA],
XT [auth XA],
XU [auth XA],
XV [auth YA],
XW [auth YA],
XX [auth YA],
XY [auth YA],
XZ [auth YA],
YAA [auth YA],
YBA [auth YA],
YCA [auth YA],
YD [auth QA],
YDA [auth YA],
YE [auth QA],
YEA [auth YA],
YF [auth RA],
YFA [auth YA],
YG [auth RA],
YGA [auth YA],
YH [auth RA],
YHA [auth YA],
YI [auth RA],
YIA [auth YA],
YJ [auth RA],
YK [auth RA],
YL [auth RA],
YM [auth RA],
YN [auth RA],
YO [auth RA],
YP [auth RA],
YQ [auth RA],
YR [auth RA],
YS [auth XA],
YT [auth XA],
YU [auth XA],
YV [auth YA],
YW [auth YA],
YX [auth YA],
YY [auth YA],
YZ [auth YA],
ZAA [auth YA],
ZBA [auth YA],
ZCA [auth YA],
ZD [auth QA],
ZDA [auth YA],
ZE [auth QA],
ZEA [auth YA],
ZF [auth RA],
ZFA [auth YA],
ZG [auth RA],
ZGA [auth YA],
ZH [auth RA],
ZHA [auth YA],
ZI [auth RA],
ZIA [auth YA],
ZJ [auth RA],
ZK [auth RA],
ZL [auth RA],
ZM [auth RA],
ZN [auth RA],
ZO [auth RA],
ZP [auth RA],
ZQ [auth RA],
ZR [auth RA],
ZS [auth XA],
ZT [auth XA],
ZU [auth XA],
ZV [auth YA],
ZW [auth YA],
ZX [auth YA],
ZY [auth YA],
ZZ [auth YA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.719α = 90
b = 449.479β = 90
c = 617.344γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM093278

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary