4LFZ

Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U in the Absence of Paromomycin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.92 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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This is version 2.1 of the entry. See complete history. 


Literature

Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops.

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

(2014) Proc Natl Acad Sci U S A 111: 12740-12745

  • DOI: https://doi.org/10.1073/pnas.1409436111
  • Primary Citation of Related Structures:  
    1VVJ, 4L47, 4L71, 4LEL, 4LFZ, 4LNT, 4LSK, 4LT8, 4P70

  • PubMed Abstract: 

    Maintenance of the correct reading frame on the ribosome is essential for accurate protein synthesis. Here, we report structures of the 70S ribosome bound to frameshift suppressor tRNA(SufA6) and N1-methylguanosine at position 37 (m(1)G37) modification-deficient anticodon stem loop(Pro), both of which cause the ribosome to decode 4 rather than 3 nucleotides, resulting in a +1 reading frame. Our results reveal that decoding at +1 suppressible codons causes suppressor tRNA(SufA6) to undergo a rearrangement of its 5' stem that destabilizes U32, thereby disrupting the conserved U32-A38 base pair. Unexpectedly, the removal of the m(1)G37 modification of tRNA(Pro) also disrupts U32-A38 pairing in a structurally analogous manner. The lack of U32-A38 pairing provides a structural correlation between the transition from canonical translation and a +1 reading of the mRNA. Our structures clarify the molecular mechanism behind suppressor tRNA-induced +1 frameshifting and advance our understanding of the role played by the ribosome in maintaining the correct translational reading frame.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth QB],
EB [auth XB]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth QC],
FB [auth XC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth QD],
GB [auth XD]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth QE],
HB [auth XE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth QF],
IB [auth XF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth QG],
JB [auth XG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth QH],
KB [auth XH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth QI],
LB [auth XI]		128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth QJ],
MB [auth XJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth QK],
NB [auth XK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth QL],
OB [auth XL]		132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth QM],
PB [auth XM]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth QN],
QB [auth XN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth QO],
RB [auth XO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth QP],
SB [auth XP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth QQ],
TB [auth XQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth QR],
UB [auth XR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth QS],
VB [auth XS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth QT],
WB [auth XT]		106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth QU],
XB [auth XU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth RD],
DC [auth YD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3BA [auth RE],
EC [auth YE]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth RF],
FC [auth YF]		210Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5DA [auth RG],
GC [auth YG]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6EA [auth RH],
HC [auth YH]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth RI],
IC [auth YI]		148Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13GA [auth RN],
JC [auth YN]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14HA [auth RO],
KC [auth YO]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15IA [auth RP],
LC [auth YP]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16JA [auth RQ],
MC [auth YQ]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17KA [auth RR],
NC [auth YR]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18LA [auth RS],
OC [auth YS]		112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19MA [auth RT],
PC [auth YT]		146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20NA [auth RU],
QC [auth YU]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21OA [auth RV],
RC [auth YV]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PA [auth RW],
SC [auth YW]		113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23QA [auth RX],
TC [auth YX]		96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24RA [auth RY],
UC [auth YY]		110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25SA [auth RZ],
VC [auth YZ]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27TA [auth R0],
WC [auth Y0]		85Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28UA [auth R1],
XC [auth Y1]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29VA [auth R2],
YC [auth Y2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30WA [auth R3],
ZC [auth Y3]		60Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31AD [auth Y4],
XA [auth R4]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BD [auth Y5],
YA [auth R5]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CD [auth Y6],
ZA [auth R6]		54Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth R7],
DD [auth Y7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth R8],
ED [auth Y8]		65Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth R9],
FD [auth Y9]		37Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth QA],
DB [auth XA]		1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-site tRNA fMetV [auth QV],
YB [auth XV]		77Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
A-site ASL SufA6W [auth QX],
ZB [auth XX]		25synthetic construct
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Entity ID: 24
MoleculeChains LengthOrganismImage
messenger RNAAC [auth XY],
X [auth QY]		18synthetic construct
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S rRNABC [auth YA],
Y [auth RA]		2,916Thermus thermophilus HB8
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S rRNACC [auth YB],
Z [auth RB]		122Thermus thermophilus HB8
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Entity ID: 56
MoleculeChains LengthOrganismImage
tRNA acceptor end mimicGD [auth Z6],
HD [auth Z8]		3synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP
Download Ideal Coordinates CCD File 
TS [auth XX]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
MDA [auth Y9]
OS [auth XD]
QS [auth XN]
SP [auth R9]
UF [auth QD]
MDA [auth Y9],
OS [auth XD],
QS [auth XN],
SP [auth R9],
UF [auth QD],
YF [auth QN]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
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],
AF [auth QA],
AG [auth QX],
AH [auth RA],
AI [auth RA],
AJ [auth RA],
AK [auth RA],
AL [auth RA],
AM [auth RA],
AN [auth RA],
AO [auth RA],
AP [auth RA],
AQ [auth XA],
AR [auth XA],
AS [auth XA],
AT [auth YA],
AU [auth YA],
AV [auth YA],
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],
BF [auth QA],
BG [auth RA],
BH [auth RA],
BI [auth RA],
BJ [auth RA],
BK [auth RA],
BL [auth RA],
BM [auth RA],
BN [auth RA],
BO [auth RA],
BP [auth RA],
BQ [auth XA],
BR [auth XA],
BS [auth XA],
BT [auth YA],
BU [auth YA],
BV [auth YA],
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],
CF [auth QA],
CG [auth RA],
CH [auth RA],
CI [auth RA],
CJ [auth RA],
CK [auth RA],
CL [auth RA],
CM [auth RA],
CN [auth RA],
CO [auth RA],
CP [auth RA],
CQ [auth XA],
CR [auth XA],
CS [auth XA],
CT [auth YA],
CU [auth YA],
CV [auth YA],
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],
DF [auth QA],
DG [auth RA],
DH [auth RA],
DI [auth RA],
DJ [auth RA],
DK [auth RA],
DL [auth RA],
DM [auth RA],
DN [auth RA],
DO [auth RA],
DP [auth RA],
DQ [auth XA],
DR [auth XA],
DS [auth XA],
DT [auth YA],
DU [auth YA],
DV [auth YA],
DW [auth YA],
DX [auth YA],
DY [auth YA],
DZ [auth YA],
EAA [auth YA],
EBA [auth YA],
ECA [auth YA],
EDA [auth YB],
EE [auth QA],
EF [auth QA],
EG [auth RA],
EH [auth RA],
EI [auth RA],
EJ [auth RA],
EK [auth RA],
EL [auth RA],
EM [auth RA],
EN [auth RA],
EO [auth RA],
EP [auth RA],
EQ [auth XA],
ER [auth XA],
ES [auth XA],
ET [auth YA],
EU [auth YA],
EV [auth YA],
EW [auth YA],
EX [auth YA],
EY [auth YA],
EZ [auth YA],
FAA [auth YA],
FBA [auth YA],
FCA [auth YA],
FDA [auth YB],
FE [auth QA],
FF [auth QA],
FG [auth RA],
FH [auth RA],
FI [auth RA],
FJ [auth RA],
FK [auth RA],
FL [auth RA],
FM [auth RA],
FN [auth RA],
FO [auth RA],
FP [auth RA],
FQ [auth XA],
FR [auth XA],
FS [auth XA],
FT [auth YA],
FU [auth YA],
FV [auth YA],
FW [auth YA],
FX [auth YA],
FY [auth YA],
FZ [auth YA],
GAA [auth YA],
GBA [auth YA],
GCA [auth YA],
GDA [auth YB],
GE [auth QA],
GF [auth QA],
GG [auth RA],
GH [auth RA],
GI [auth RA],
GJ [auth RA],
GK [auth RA],
GL [auth RA],
GM [auth RA],
GN [auth RA],
GO [auth RA],
GP [auth RB],
GQ [auth XA],
GR [auth XA],
GS [auth XA],
GT [auth YA],
GU [auth YA],
GV [auth YA],
GW [auth YA],
GX [auth YA],
GY [auth YA],
GZ [auth YA],
HAA [auth YA],
HBA [auth YA],
HCA [auth YA],
HDA [auth YE],
HE [auth QA],
HF [auth QA],
HG [auth RA],
HH [auth RA],
HI [auth RA],
HJ [auth RA],
HK [auth RA],
HL [auth RA],
HM [auth RA],
HN [auth RA],
HO [auth RA],
HP [auth RB],
HQ [auth XA],
HR [auth XA],
HS [auth XA],
HT [auth YA],
HU [auth YA],
HV [auth YA],
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 YP],
IE [auth QA],
IF [auth QA],
IG [auth RA],
IH [auth RA],
II [auth RA],
IJ [auth RA],
IK [auth RA],
IL [auth RA],
IM [auth RA],
IN [auth RA],
IO [auth RA],
IP [auth RD],
IQ [auth XA],
IR [auth XA],
IS [auth XA],
IT [auth YA],
IU [auth YA],
IV [auth YA],
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 YQ],
JE [auth QA],
JF [auth QA],
JG [auth RA],
JH [auth RA],
JI [auth RA],
JJ [auth RA],
JK [auth RA],
JL [auth RA],
JM [auth RA],
JN [auth RA],
JO [auth RA],
JP [auth RE],
JQ [auth XA],
JR [auth XA],
JS [auth XA],
JT [auth YA],
JU [auth YA],
JV [auth YA],
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 Y5],
KE [auth QA],
KF [auth QA],
KG [auth RA],
KH [auth RA],
KI [auth RA],
KJ [auth RA],
KK [auth RA],
KL [auth RA],
KM [auth RA],
KN [auth RA],
KO [auth RA],
KP [auth RE],
KQ [auth XA],
KR [auth XA],
KS [auth XA],
KT [auth YA],
KU [auth YA],
KV [auth YA],
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 Y7],
LE [auth QA],
LF [auth QA],
LG [auth RA],
LH [auth RA],
LI [auth RA],
LJ [auth RA],
LK [auth RA],
LL [auth RA],
LM [auth RA],
LN [auth RA],
LO [auth RA],
LP [auth RF],
LQ [auth XA],
LR [auth XA],
LS [auth XA],
LT [auth YA],
LU [auth YA],
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],
ME [auth QA],
MF [auth QA],
MG [auth RA],
MH [auth RA],
MI [auth RA],
MJ [auth RA],
MK [auth RA],
ML [auth RA],
MM [auth RA],
MN [auth RA],
MO [auth RA],
MP [auth RP],
MQ [auth XA],
MR [auth XA],
MS [auth XA],
MT [auth YA],
MU [auth YA],
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],
NE [auth QA],
NF [auth QA],
NG [auth RA],
NH [auth RA],
NI [auth RA],
NJ [auth RA],
NK [auth RA],
NL [auth RA],
NM [auth RA],
NN [auth RA],
NO [auth RA],
NP [auth RR],
NQ [auth XA],
NR [auth XA],
NS [auth XB],
NT [auth YA],
NU [auth YA],
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],
OE [auth QA],
OF [auth QA],
OG [auth RA],
OH [auth RA],
OI [auth RA],
OJ [auth RA],
OK [auth RA],
OL [auth RA],
OM [auth RA],
ON [auth RA],
OO [auth RA],
OP [auth RR],
OQ [auth XA],
OR [auth XA],
OT [auth YA],
OU [auth YA],
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],
PE [auth QA],
PF [auth QA],
PG [auth RA],
PH [auth RA],
PI [auth RA],
PJ [auth RA],
PK [auth RA],
PL [auth RA],
PM [auth RA],
PN [auth RA],
PO [auth RA],
PP [auth R0],
PQ [auth XA],
PR [auth XA],
PS [auth XM],
PT [auth YA],
PU [auth YA],
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],
QE [auth QA],
QF [auth QA],
QG [auth RA],
QH [auth RA],
QI [auth RA],
QJ [auth RA],
QK [auth RA],
QL [auth RA],
QM [auth RA],
QN [auth RA],
QO [auth RA],
QP [auth R5],
QQ [auth XA],
QR [auth XA],
QT [auth YA],
QU [auth YA],
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],
RE [auth QA],
RF [auth QA],
RG [auth RA],
RH [auth RA],
RI [auth RA],
RJ [auth RA],
RK [auth RA],
RL [auth RA],
RM [auth RA],
RN [auth RA],
RO [auth RA],
RP [auth R8],
RQ [auth XA],
RR [auth XA],
RS [auth XV],
RT [auth YA],
RU [auth YA],
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],
SE [auth QA],
SF [auth QA],
SG [auth RA],
SH [auth RA],
SI [auth RA],
SJ [auth RA],
SK [auth RA],
SL [auth RA],
SM [auth RA],
SN [auth RA],
SO [auth RA],
SQ [auth XA],
SR [auth XA],
SS [auth XV],
ST [auth YA],
SU [auth YA],
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],
TE [auth QA],
TF [auth QA],
TG [auth RA],
TH [auth RA],
TI [auth RA],
TJ [auth RA],
TK [auth RA],
TL [auth RA],
TM [auth RA],
TN [auth RA],
TO [auth RA],
TP [auth XA],
TQ [auth XA],
TR [auth XA],
TT [auth YA],
TU [auth YA],
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],
UE [auth QA],
UG [auth RA],
UH [auth RA],
UI [auth RA],
UJ [auth RA],
UK [auth RA],
UL [auth RA],
UM [auth RA],
UN [auth RA],
UO [auth RA],
UP [auth XA],
UQ [auth XA],
UR [auth XA],
US [auth XX],
UT [auth YA],
UU [auth YA],
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],
VE [auth QA],
VF [auth QF],
VG [auth RA],
VH [auth RA],
VI [auth RA],
VJ [auth RA],
VK [auth RA],
VL [auth RA],
VM [auth RA],
VN [auth RA],
VO [auth RA],
VP [auth XA],
VQ [auth XA],
VR [auth XA],
VS [auth YA],
VT [auth YA],
VU [auth YA],
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],
WE [auth QA],
WF [auth QH],
WG [auth RA],
WH [auth RA],
WI [auth RA],
WJ [auth RA],
WK [auth RA],
WL [auth RA],
WM [auth RA],
WN [auth RA],
WO [auth RA],
WP [auth XA],
WQ [auth XA],
WR [auth XA],
WS [auth YA],
WT [auth YA],
WU [auth YA],
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],
XE [auth QA],
XF [auth QM],
XG [auth RA],
XH [auth RA],
XI [auth RA],
XJ [auth RA],
XK [auth RA],
XL [auth RA],
XM [auth RA],
XN [auth RA],
XO [auth RA],
XP [auth XA],
XQ [auth XA],
XR [auth XA],
XS [auth YA],
XT [auth YA],
XU [auth YA],
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],
YE [auth QA],
YG [auth RA],
YH [auth RA],
YI [auth RA],
YJ [auth RA],
YK [auth RA],
YL [auth RA],
YM [auth RA],
YN [auth RA],
YO [auth RA],
YP [auth XA],
YQ [auth XA],
YR [auth XA],
YS [auth YA],
YT [auth YA],
YU [auth YA],
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],
ZE [auth QA],
ZF [auth QV],
ZG [auth RA],
ZH [auth RA],
ZI [auth RA],
ZJ [auth RA],
ZK [auth RA],
ZL [auth RA],
ZM [auth RA],
ZN [auth RA],
ZO [auth RA],
ZP [auth XA],
ZQ [auth XA],
ZR [auth XA],
ZS [auth YA],
ZT [auth YA],
ZU [auth YA],
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: 3.92 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.375α = 90
b = 451.022β = 90
c = 621.092γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references
  • Version 1.2: 2014-09-24
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Other
  • Version 2.0: 2024-05-29
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Structure summary