4TUA

Crystal structure of ASL-Thr bound to Codon ACC-A on the Ribosome

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Models: experimental
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This is version 2.2 of the entry. See complete history. 


Literature

Structural insights into translational recoding by frameshift suppressor tRNASufJ.

Fagan, C.E., Maehigashi, T., Dunkle, J.A., Miles, S.J., Dunham, C.M.

(2014) RNA 20: 1944-1954

  • DOI: https://doi.org/10.1261/rna.046953.114
  • Primary Citation of Related Structures:  
    4TUA, 4TUB, 4TUC, 4TUD, 4TUE

  • PubMed Abstract: 

    The three-nucleotide mRNA reading frame is tightly regulated during translation to ensure accurate protein expression. Translation errors that lead to aberrant protein production can result from the uncoupled movement of the tRNA in either the 5' or 3' direction on mRNA. Here, we report the biochemical and structural characterization of +1 frameshift suppressor tRNA(SufJ), a tRNA known to decode four, instead of three, nucleotides. Frameshift suppressor tRNA(SufJ) contains an insertion 5' to its anticodon, expanding the anticodon loop from seven to eight nucleotides. Our results indicate that the expansion of the anticodon loop of either ASL(SufJ) or tRNA(SufJ) does not affect its affinity for the A site of the ribosome. Structural analyses of both ASL(SufJ) and ASL(Thr) bound to the Thermus thermophilus 70S ribosome demonstrate both ASLs decode in the zero frame. Although the anticodon loop residues 34-37 are superimposable with canonical seven-nucleotide ASLs, the single C31.5 insertion between nucleotides 31 and 32 in ASL(SufJ) imposes a conformational change of the anticodon stem, that repositions and tilts the ASL toward the back of the A site. Further modeling analyses reveal that this tilting would cause a distortion in full-length A-site tRNA(SufJ) during tRNA selection and possibly impede gripping of the anticodon stem by 16S rRNA nucleotides in the P site. Together, these data implicate tRNA distortion as a major driver of noncanonical translation events such as frameshifting.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth QB],
FB [auth XB]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth QC],
GB [auth XC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth QD],
HB [auth XD]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth QE],
IB [auth XE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth QF],
JB [auth XF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth QG],
KB [auth XG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth QH],
LB [auth XH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth QI],
MB [auth XI]		128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth QJ],
NB [auth XJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth QK],
OB [auth XK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth QL],
PB [auth XL]		132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth QM],
QB [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],
RB [auth XN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth QO],
SB [auth XO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth QP],
TB [auth XP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth QQ],
UB [auth XQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth QR],
VB [auth XR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth QS],
WB [auth XS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth QT],
XB [auth XT]		106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth QU],
YB [auth XU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth RD],
EC [auth YD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3BA [auth RE],
FC [auth YE]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth RF],
GC [auth YF]		210Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5DA [auth RG],
HC [auth YG]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6EA [auth RH],
IC [auth YH]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth RI],
JC [auth YI]		148Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13GA [auth RN],
KC [auth YN]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14HA [auth RO],
LC [auth YO]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15IA [auth RP],
MC [auth YP]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16JA [auth RQ],
NC [auth YQ]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17KA [auth RR],
OC [auth YR]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18LA [auth RS],
PC [auth YS]		112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19MA [auth RT],
QC [auth YT]		146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20NA [auth RU],
RC [auth YU]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21OA [auth RV],
SC [auth YV]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PA [auth RW],
TC [auth YW]		113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23QA [auth RX],
UC [auth YX]		96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24RA [auth RY],
VC [auth YY]		110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25SA [auth RZ],
WC [auth YZ]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27TA [auth R0],
XC [auth Y0]		85Thermus thermophilus HB8Mutation(s): 0 
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UniProt GroupP60493
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28UA [auth R1],
YC [auth Y1]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29VA [auth R2],
ZC [auth Y2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AD [auth Y3],
WA [auth R3]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31BD [auth Y4],
XA [auth R4]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CD [auth Y5],
YA [auth R5]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33DD [auth Y6],
ZA [auth R6]		54Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth R7],
ED [auth Y7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth R8],
FD [auth Y8]		65Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth R9],
GD [auth Y9]		37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth QA],
EB [auth XA]		1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-site tRNA-fMetV [auth QV],
ZB [auth XV]		77Escherichia coli str. K-12 substr. DH10B
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Entity ID: 23
MoleculeChains LengthOrganismImage
messenger RNAAC [auth XX],
W [auth QX]		25synthetic construct
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Entity ID: 24
MoleculeChains LengthOrganismImage
A-site ASL-ThrBC [auth XY],
X [auth QY]		17synthetic construct
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S rRNACC [auth YA],
Y [auth RA]		2,915Thermus thermophilus HB8
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S rRNADC [auth YB],
Z [auth RB]		122Thermus thermophilus HB8
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Entity ID: 56
MoleculeChains LengthOrganismImage
CC-PuroDB [auth Z5],
HD [auth Z6]		3synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR
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EY [auth XA],
ZG [auth QA]		PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN
Query on ZN
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AH [auth QD],
EH [auth QN],
FY [auth XD],
HY [auth XN]		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 QA],
AGA [auth YA],
AHA [auth YA],
AI [auth RA],
AIA [auth YA],
AJ [auth RA],
AJA [auth YA],
AK [auth RA],
AKA [auth YA],
AL [auth RA],
ALA [auth YA],
AM [auth RA],
AN [auth RA],
AO [auth RA],
AP [auth RA],
AQ [auth RA],
AR [auth RA],
AS [auth RA],
AT [auth RA],
AU [auth XA],
AV [auth XA],
AW [auth XA],
AX [auth XA],
AY [auth XA],
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 QA],
BGA [auth YA],
BH [auth QE],
BHA [auth YA],
BI [auth RA],
BIA [auth YA],
BJ [auth RA],
BJA [auth YA],
BK [auth RA],
BKA [auth YA],
BL [auth RA],
BLA [auth YA],
BM [auth RA],
BN [auth RA],
BO [auth RA],
BP [auth RA],
BQ [auth RA],
BR [auth RA],
BS [auth RA],
BT [auth RA],
BU [auth XA],
BV [auth XA],
BW [auth XA],
BX [auth XA],
BY [auth XA],
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 QA],
CGA [auth YA],
CH [auth QF],
CHA [auth YA],
CI [auth RA],
CIA [auth YA],
CJ [auth RA],
CJA [auth YA],
CK [auth RA],
CKA [auth YA],
CL [auth RA],
CLA [auth YA],
CM [auth RA],
CN [auth RA],
CO [auth RA],
CP [auth RA],
CQ [auth RA],
CR [auth RA],
CS [auth RA],
CT [auth RA],
CU [auth XA],
CV [auth XA],
CW [auth XA],
CX [auth XA],
CY [auth XA],
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 QA],
DGA [auth YA],
DH [auth QM],
DHA [auth YA],
DI [auth RA],
DIA [auth YA],
DJ [auth RA],
DJA [auth YA],
DK [auth RA],
DKA [auth YA],
DL [auth RA],
DLA [auth YA],
DM [auth RA],
DN [auth RA],
DO [auth RA],
DP [auth RA],
DQ [auth RA],
DR [auth RA],
DS [auth RA],
DT [auth RA],
DU [auth XA],
DV [auth XA],
DW [auth XA],
DX [auth XA],
DY [auth XA],
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 QA],
EGA [auth YA],
EHA [auth YA],
EI [auth RA],
EIA [auth YA],
EJ [auth RA],
EJA [auth YA],
EK [auth RA],
EKA [auth YA],
EL [auth RA],
ELA [auth YA],
EM [auth RA],
EN [auth RA],
EO [auth RA],
EP [auth RA],
EQ [auth RA],
ER [auth RA],
ES [auth RA],
ET [auth RA],
EU [auth XA],
EV [auth XA],
EW [auth XA],
EX [auth XA],
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 QA],
FGA [auth YA],
FH [auth QV],
FHA [auth YA],
FI [auth RA],
FIA [auth YA],
FJ [auth RA],
FJA [auth YA],
FK [auth RA],
FKA [auth YA],
FL [auth RA],
FLA [auth YA],
FM [auth RA],
FN [auth RA],
FO [auth RA],
FP [auth RA],
FQ [auth RA],
FR [auth RA],
FS [auth RA],
FT [auth RA],
FU [auth XA],
FV [auth XA],
FW [auth XA],
FX [auth XA],
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 QA],
GGA [auth YA],
GH [auth QV],
GHA [auth YA],
GI [auth RA],
GIA [auth YA],
GJ [auth RA],
GJA [auth YA],
GK [auth RA],
GKA [auth YA],
GL [auth RA],
GLA [auth YA],
GM [auth RA],
GN [auth RA],
GO [auth RA],
GP [auth RA],
GQ [auth RA],
GR [auth RA],
GS [auth RA],
GT [auth RB],
GU [auth XA],
GV [auth XA],
GW [auth XA],
GX [auth XA],
GY [auth XF],
GZ [auth YA],
HAA [auth YA],
HBA [auth YA],
HCA [auth YA],
HDA [auth YA],
HE [auth QA],
HEA [auth YA],
HF [auth QA],
HFA [auth YA],
HG [auth QA],
HGA [auth YA],
HH [auth QV],
HHA [auth YA],
HI [auth RA],
HIA [auth YA],
HJ [auth RA],
HJA [auth YA],
HK [auth RA],
HKA [auth YA],
HL [auth RA],
HLA [auth YA],
HM [auth RA],
HN [auth RA],
HO [auth RA],
HP [auth RA],
HQ [auth RA],
HR [auth RA],
HS [auth RA],
HT [auth RB],
HU [auth XA],
HV [auth XA],
HW [auth XA],
HX [auth XA],
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 QA],
IGA [auth YA],
IH [auth QX],
IHA [auth YA],
II [auth RA],
IIA [auth YA],
IJ [auth RA],
IJA [auth YA],
IK [auth RA],
IKA [auth YA],
IL [auth RA],
ILA [auth YA],
IM [auth RA],
IN [auth RA],
IO [auth RA],
IP [auth RA],
IQ [auth RA],
IR [auth RA],
IS [auth RA],
IT [auth RB],
IU [auth XA],
IV [auth XA],
IW [auth XA],
IX [auth XA],
IY [auth XV],
IZ [auth YA],
JAA [auth YA],
JBA [auth YA],
JCA [auth YA],
JD [auth QA],
JDA [auth YA],
JE [auth QA],
JEA [auth YA],
JF [auth QA],
JFA [auth YA],
JG [auth QA],
JGA [auth YA],
JH [auth QX],
JHA [auth YA],
JI [auth RA],
JIA [auth YA],
JJ [auth RA],
JJA [auth YA],
JK [auth RA],
JKA [auth YA],
JL [auth RA],
JLA [auth YA],
JM [auth RA],
JN [auth RA],
JO [auth RA],
JP [auth RA],
JQ [auth RA],
JR [auth RA],
JS [auth RA],
JT [auth RB],
JU [auth XA],
JV [auth XA],
JW [auth XA],
JX [auth XA],
JY [auth XV],
JZ [auth YA],
KAA [auth YA],
KBA [auth YA],
KCA [auth YA],
KD [auth QA],
KDA [auth YA],
KE [auth QA],
KEA [auth YA],
KF [auth QA],
KFA [auth YA],
KG [auth QA],
KGA [auth YA],
KH [auth QY],
KHA [auth YA],
KI [auth RA],
KIA [auth YA],
KJ [auth RA],
KJA [auth YA],
KK [auth RA],
KKA [auth YA],
KL [auth RA],
KLA [auth YA],
KM [auth RA],
KN [auth RA],
KO [auth RA],
KP [auth RA],
KQ [auth RA],
KR [auth RA],
KS [auth RA],
KT [auth RB],
KU [auth XA],
KV [auth XA],
KW [auth XA],
KX [auth XA],
KY [auth XV],
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 QA],
LFA [auth YA],
LG [auth QA],
LGA [auth YA],
LH [auth RA],
LHA [auth YA],
LI [auth RA],
LIA [auth YA],
LJ [auth RA],
LJA [auth YA],
LK [auth RA],
LKA [auth YA],
LL [auth RA],
LLA [auth YA],
LM [auth RA],
LN [auth RA],
LO [auth RA],
LP [auth RA],
LQ [auth RA],
LR [auth RA],
LS [auth RA],
LT [auth RD],
LU [auth XA],
LV [auth XA],
LW [auth XA],
LX [auth XA],
LY [auth XX],
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 QA],
MFA [auth YA],
MG [auth QA],
MGA [auth YA],
MH [auth RA],
MHA [auth YA],
MI [auth RA],
MIA [auth YA],
MJ [auth RA],
MJA [auth YA],
MK [auth RA],
MKA [auth YA],
ML [auth RA],
MLA [auth YB],
MM [auth RA],
MN [auth RA],
MO [auth RA],
MP [auth RA],
MQ [auth RA],
MR [auth RA],
MS [auth RA],
MT [auth RE],
MU [auth XA],
MV [auth XA],
MW [auth XA],
MX [auth XA],
MY [auth XX],
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 QA],
NFA [auth YA],
NG [auth QA],
NGA [auth YA],
NH [auth RA],
NHA [auth YA],
NI [auth RA],
NIA [auth YA],
NJ [auth RA],
NJA [auth YA],
NK [auth RA],
NKA [auth YA],
NL [auth RA],
NLA [auth YB],
NM [auth RA],
NN [auth RA],
NO [auth RA],
NP [auth RA],
NQ [auth RA],
NR [auth RA],
NS [auth RA],
NT [auth RE],
NU [auth XA],
NV [auth XA],
NW [auth XA],
NX [auth XA],
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 QA],
OFA [auth YA],
OG [auth QA],
OGA [auth YA],
OH [auth RA],
OHA [auth YA],
OI [auth RA],
OIA [auth YA],
OJ [auth RA],
OJA [auth YA],
OK [auth RA],
OKA [auth YA],
OL [auth RA],
OLA [auth YB],
OM [auth RA],
ON [auth RA],
OO [auth RA],
OP [auth RA],
OQ [auth RA],
OR [auth RA],
OS [auth RA],
OT [auth RF],
OU [auth XA],
OV [auth XA],
OW [auth XA],
OX [auth XA],
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 QA],
PFA [auth YA],
PG [auth QA],
PGA [auth YA],
PH [auth RA],
PHA [auth YA],
PI [auth RA],
PIA [auth YA],
PJ [auth RA],
PJA [auth YA],
PK [auth RA],
PKA [auth YA],
PL [auth RA],
PLA [auth YD],
PM [auth RA],
PN [auth RA],
PO [auth RA],
PP [auth RA],
PQ [auth RA],
PR [auth RA],
PS [auth RA],
PT [auth RR],
PU [auth XA],
PV [auth XA],
PW [auth XA],
PX [auth XA],
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 QA],
QFA [auth YA],
QG [auth QA],
QGA [auth YA],
QH [auth RA],
QHA [auth YA],
QI [auth RA],
QIA [auth YA],
QJ [auth RA],
QJA [auth YA],
QK [auth RA],
QKA [auth YA],
QL [auth RA],
QLA [auth YE],
QM [auth RA],
QN [auth RA],
QO [auth RA],
QP [auth RA],
QQ [auth RA],
QR [auth RA],
QS [auth RA],
QT [auth R0],
QU [auth XA],
QV [auth XA],
QW [auth XA],
QX [auth XA],
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 QA],
RFA [auth YA],
RG [auth QA],
RGA [auth YA],
RH [auth RA],
RHA [auth YA],
RI [auth RA],
RIA [auth YA],
RJ [auth RA],
RJA [auth YA],
RK [auth RA],
RKA [auth YA],
RL [auth RA],
RLA [auth YE],
RM [auth RA],
RN [auth RA],
RO [auth RA],
RP [auth RA],
RQ [auth RA],
RR [auth RA],
RS [auth RA],
RT [auth R1],
RU [auth XA],
RV [auth XA],
RW [auth XA],
RX [auth XA],
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 QA],
SFA [auth YA],
SG [auth QA],
SGA [auth YA],
SH [auth RA],
SHA [auth YA],
SI [auth RA],
SIA [auth YA],
SJ [auth RA],
SJA [auth YA],
SK [auth RA],
SKA [auth YA],
SL [auth RA],
SLA [auth YP],
SM [auth RA],
SN [auth RA],
SO [auth RA],
SP [auth RA],
SQ [auth RA],
SR [auth RA],
SS [auth RA],
ST [auth R5],
SU [auth XA],
SV [auth XA],
SW [auth XA],
SX [auth XA],
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 QA],
TFA [auth YA],
TG [auth QA],
TGA [auth YA],
TH [auth RA],
THA [auth YA],
TI [auth RA],
TIA [auth YA],
TJ [auth RA],
TJA [auth YA],
TK [auth RA],
TKA [auth YA],
TL [auth RA],
TLA [auth YP],
TM [auth RA],
TN [auth RA],
TO [auth RA],
TP [auth RA],
TQ [auth RA],
TR [auth RA],
TS [auth RA],
TT [auth R8],
TU [auth XA],
TV [auth XA],
TW [auth XA],
TX [auth XA],
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 QA],
UFA [auth YA],
UG [auth QA],
UGA [auth YA],
UH [auth RA],
UHA [auth YA],
UI [auth RA],
UIA [auth YA],
UJ [auth RA],
UJA [auth YA],
UK [auth RA],
UKA [auth YA],
UL [auth RA],
ULA [auth YQ],
UM [auth RA],
UN [auth RA],
UO [auth RA],
UP [auth RA],
UQ [auth RA],
UR [auth RA],
US [auth RA],
UT [auth XA],
UU [auth XA],
UV [auth XA],
UW [auth XA],
UX [auth XA],
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 QA],
VFA [auth YA],
VG [auth QA],
VGA [auth YA],
VH [auth RA],
VHA [auth YA],
VI [auth RA],
VIA [auth YA],
VJ [auth RA],
VJA [auth YA],
VK [auth RA],
VKA [auth YA],
VL [auth RA],
VLA [auth Y0],
VM [auth RA],
VN [auth RA],
VO [auth RA],
VP [auth RA],
VQ [auth RA],
VR [auth RA],
VS [auth RA],
VT [auth XA],
VU [auth XA],
VV [auth XA],
VW [auth XA],
VX [auth XA],
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 QA],
WFA [auth YA],
WG [auth QA],
WGA [auth YA],
WH [auth RA],
WHA [auth YA],
WI [auth RA],
WIA [auth YA],
WJ [auth RA],
WJA [auth YA],
WK [auth RA],
WKA [auth YA],
WL [auth RA],
WLA [auth Y0],
WM [auth RA],
WN [auth RA],
WO [auth RA],
WP [auth RA],
WQ [auth RA],
WR [auth RA],
WS [auth RA],
WT [auth XA],
WU [auth XA],
WV [auth XA],
WW [auth XA],
WX [auth XA],
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 QA],
XFA [auth YA],
XG [auth QA],
XGA [auth YA],
XH [auth RA],
XHA [auth YA],
XI [auth RA],
XIA [auth YA],
XJ [auth RA],
XJA [auth YA],
XK [auth RA],
XKA [auth YA],
XL [auth RA],
XLA [auth Y0],
XM [auth RA],
XN [auth RA],
XO [auth RA],
XP [auth RA],
XQ [auth RA],
XR [auth RA],
XS [auth RA],
XT [auth XA],
XU [auth XA],
XV [auth XA],
XW [auth XA],
XX [auth XA],
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 QA],
YFA [auth YA],
YG [auth QA],
YGA [auth YA],
YH [auth RA],
YHA [auth YA],
YI [auth RA],
YIA [auth YA],
YJ [auth RA],
YJA [auth YA],
YK [auth RA],
YKA [auth YA],
YL [auth RA],
YLA [auth Y5],
YM [auth RA],
YN [auth RA],
YO [auth RA],
YP [auth RA],
YQ [auth RA],
YR [auth RA],
YS [auth RA],
YT [auth XA],
YU [auth XA],
YV [auth XA],
YW [auth XA],
YX [auth XA],
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 QA],
ZFA [auth YA],
ZGA [auth YA],
ZH [auth RA],
ZHA [auth YA],
ZI [auth RA],
ZIA [auth YA],
ZJ [auth RA],
ZJA [auth YA],
ZK [auth RA],
ZKA [auth YA],
ZL [auth RA],
ZLA [auth Y7],
ZM [auth RA],
ZN [auth RA],
ZO [auth RA],
ZP [auth RA],
ZQ [auth RA],
ZR [auth RA],
ZS [auth RA],
ZT [auth XA],
ZU [auth XA],
ZV [auth XA],
ZW [auth XA],
ZX [auth XA],
ZY [auth YA],
ZZ [auth YA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.977α = 90
b = 448.713β = 90
c = 621.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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 StatesR01GM093279
National Defense Science and Engineering Graduate Fellowship ProgramUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM8367

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 2.0: 2022-04-13
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary