1KC8

Co-crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit

Hansen, J.Moore, P.B.Steitz, T.A.

(2003) J Mol Biol 330: 1061-1075

  • DOI: https://doi.org/10.1016/s0022-2836(03)00668-5
  • Primary Citation of Related Structures:  
    1K73, 1KC8, 1N8R, 1NJI

  • PubMed Abstract: 

    Structures of anisomycin, chloramphenicol, sparsomycin, blasticidin S, and virginiamycin M bound to the large ribosomal subunit of Haloarcula marismortui have been determined at 3.0A resolution. Most of these antibiotics bind to sites that overlap those of either peptidyl-tRNA or aminoacyl-tRNA, consistent with their functioning as competitive inhibitors of peptide bond formation. Two hydrophobic crevices, one at the peptidyl transferase center and the other at the entrance to the peptide exit tunnel play roles in binding these antibiotics. Midway between these crevices, nucleotide A2103 of H.marismortui (2062 Escherichia coli) varies in its conformation and thereby contacts antibiotics bound at either crevice. The aromatic ring of anisomycin binds to the active-site hydrophobic crevice, as does the aromatic ring of puromycin, while the aromatic ring of chloramphenicol binds to the exit tunnel hydrophobic crevice. Sparsomycin contacts primarily a P-site bound substrate, but also extends into the active-site hydrophobic crevice. Virginiamycin M occupies portions of both the A and P-site, and induces a conformational change in the ribosome. Blasticidin S base-pairs with the P-loop and thereby mimics C74 and C75 of a P-site bound tRNA.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2239Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P20276 
Go to UniProtKB:  P20276
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20276
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3337Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P20279 
Go to UniProtKB:  P20279
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20279
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L4246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12735 
Go to UniProtKB:  P12735
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12735
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L5176Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14124 
Go to UniProtKB:  P14124
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14124
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L6177Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14135 
Go to UniProtKB:  P14135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14135
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L7AE119Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12743 
Go to UniProtKB:  P12743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12743
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10348Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P15825 
Go to UniProtKB:  P15825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15825
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10E167Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P60617 
Go to UniProtKB:  P60617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60617
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L13145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P29198 
Go to UniProtKB:  P29198
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29198
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L14132Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P22450 
Go to UniProtKB:  P22450
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22450
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15164Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12737 
Go to UniProtKB:  P12737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12737
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15E194Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P60618 
Go to UniProtKB:  P60618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60618
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18186Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14123 
Go to UniProtKB:  P14123
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14123
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18E115Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12733 
Go to UniProtKB:  P12733
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12733
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L19E148Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14119 
Go to UniProtKB:  P14119
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14119
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L21E95Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12734 
Go to UniProtKB:  P12734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12734
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L22154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P10970 
Go to UniProtKB:  P10970
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10970
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2384Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12732 
Go to UniProtKB:  P12732
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12732
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24119Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P10972 
Go to UniProtKB:  P10972
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10972
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24E66Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14116 
Go to UniProtKB:  P14116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14116
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2970Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P10971 
Go to UniProtKB:  P10971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10971
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L30154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14121 
Go to UniProtKB:  P14121
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14121
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L31E91Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P18138 
Go to UniProtKB:  P18138
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18138
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L32E240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12736 
Go to UniProtKB:  P12736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12736
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37AeAA [auth 1]73Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P60619 
Go to UniProtKB:  P60619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60619
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37EBA [auth 2]56Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P32410 
Go to UniProtKB:  P32410
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32410
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L39ECA [auth 3]48Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P22452 
Go to UniProtKB:  P22452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22452
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L44EDA [auth 4]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P32411 
Go to UniProtKB:  P32411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32411
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
23S RRNA2,922Haloarcula marismortui
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
5S RRNA122Haloarcula marismortui
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BLS
Query on BLS

Download Ideal Coordinates CCD File 
EA [auth A],
FA [auth A]
BLASTICIDIN S
C17 H26 N8 O5
CXNPLSGKWMLZPZ-ZNIXKSQXSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
AJ [auth 1],
BJ [auth 2],
DJ [auth 4],
MI [auth P],
WI [auth V]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
ME [auth A],
NE [auth A],
OE [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CI [auth K]
DI [auth K]
EI [auth K]
EJ [auth 4]
FI [auth K]
CI [auth K],
DI [auth K],
EI [auth K],
EJ [auth 4],
FI [auth K],
IH [auth A],
II [auth M],
JH [auth A],
KH [auth A],
KI [auth N],
LH [auth A],
LI [auth O],
MH [auth A],
NH [auth A],
NI [auth P],
OH [auth A],
PH [auth A],
QH [auth A],
SI [auth S],
WH [auth C],
XH [auth D],
YI [auth Z]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
BB [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CJ [auth 4],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GI [auth L],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RH [auth B],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UH [auth C],
UI [auth U],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XI [auth Z],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZI [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AF [auth A]
AG [auth A]
AH [auth A]
AI [auth J]
BF [auth A]
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth J],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth K],
CF [auth A],
CG [auth A],
CH [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
HI [auth M],
IF [auth A],
IG [auth A],
JF [auth A],
JG [auth A],
JI [auth N],
KF [auth A],
KG [auth A],
LF [auth A],
LG [auth A],
MF [auth A],
MG [auth A],
NF [auth A],
NG [auth A],
OF [auth A],
OG [auth A],
OI [auth R],
PE [auth A],
PF [auth A],
PG [auth A],
PI [auth S],
QE [auth A],
QF [auth A],
QG [auth A],
QI [auth S],
RE [auth A],
RF [auth A],
RG [auth A],
RI [auth S],
SE [auth A],
SF [auth A],
SG [auth A],
SH [auth B],
TE [auth A],
TF [auth A],
TG [auth A],
TH [auth B],
TI [auth T],
UE [auth A],
UF [auth A],
UG [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth C],
VI [auth U],
WE [auth A],
WF [auth A],
WG [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth E],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth J]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.902α = 90
b = 300.474β = 90
c = 575.176γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description