Atomistry » Gold » PDB 1a52-3k3g » 2vyf
Atomistry »
  Gold »
    PDB 1a52-3k3g »
      2vyf »

Gold in PDB 2vyf: Crystal Structure of the Dnac

Protein crystallography data

The structure of Crystal Structure of the Dnac, PDB code: 2vyf was solved by Y.H.Lo, K.L.Tsai, Y.J.Sun, C.D.Hsiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.87 / 3.60
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 176.968, 176.968, 108.824, 90.00, 90.00, 120.00
R / Rfree (%) 29.3 / 32.4

Gold Binding Sites:

The binding sites of Gold atom in the Crystal Structure of the Dnac (pdb code 2vyf). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 4 binding sites of Gold where determined in the Crystal Structure of the Dnac, PDB code: 2vyf:
Jump to Gold binding site number: 1; 2; 3; 4;

Gold binding site 1 out of 4 in 2vyf

Go back to Gold Binding Sites List in 2vyf
Gold binding site 1 out of 4 in the Crystal Structure of the Dnac


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of the Dnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1436

b:1.0
occ:1.00
CD1 A:LEU221 2.8 0.7 1.0
CD2 A:LEU221 3.1 0.7 1.0
CG A:LEU221 3.2 0.7 1.0
ND2 A:ASN222 3.6 0.4 1.0
CA A:ALA218 3.7 0.9 1.0
CB A:ALA254 3.7 0.5 1.0
CB A:ALA218 3.9 0.4 1.0
O A:ARG250 3.9 0.3 1.0
O A:ALA218 4.0 0.9 1.0
O A:GLU434 4.2 1.0 1.0
C A:ALA218 4.3 0.9 1.0
C A:ARG250 4.4 0.3 1.0
CA A:MET251 4.4 0.1 1.0
N A:MET251 4.6 0.1 1.0
CG A:ASN222 4.6 0.4 1.0
CB A:LEU221 4.7 0.7 1.0
N A:ALA218 4.9 0.9 1.0
OD1 A:ASN222 5.0 0.4 1.0

Gold binding site 2 out of 4 in 2vyf

Go back to Gold Binding Sites List in 2vyf
Gold binding site 2 out of 4 in the Crystal Structure of the Dnac


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of the Dnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au1437

b:1.0
occ:1.00
CG A:MET249 2.8 0.5 1.0
NH2 A:ARG250 2.9 0.9 1.0
CZ A:ARG250 2.9 0.9 1.0
O A:MET249 3.0 0.3 1.0
NH1 A:ARG250 3.0 0.9 1.0
CE A:MET249 3.2 0.5 1.0
SD A:MET249 3.2 0.5 1.0
CB A:CYS253 3.3 1.0 1.0
C A:MET249 3.5 0.3 1.0
NE A:ARG250 3.7 0.9 1.0
CB A:MET249 3.9 0.5 1.0
N A:ARG250 4.1 0.3 1.0
N A:CYS253 4.2 0.5 1.0
CA A:MET249 4.2 0.3 1.0
SG A:CYS253 4.3 1.0 1.0
CA A:ARG250 4.3 0.3 1.0
CA A:CYS253 4.4 0.5 1.0
CD A:ARG250 4.5 0.9 1.0
C A:ARG250 5.0 0.3 1.0

Gold binding site 3 out of 4 in 2vyf

Go back to Gold Binding Sites List in 2vyf
Gold binding site 3 out of 4 in the Crystal Structure of the Dnac


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Crystal Structure of the Dnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au2426

b:1.0
occ:1.00
CG B:LEU1221 3.2 0.4 1.0
CD1 B:LEU1221 3.4 0.4 1.0
CD2 B:LEU1221 3.7 0.4 1.0
O B:ARG1250 3.8 0.2 1.0
CA B:ALA1218 4.1 0.8 1.0
O B:ALA1218 4.2 0.8 1.0
C B:ARG1250 4.3 0.2 1.0
CA B:MET1251 4.4 0.1 1.0
CB B:LEU1221 4.4 0.4 1.0
CB B:ALA1218 4.4 0.6 1.0
N B:ASN1222 4.4 0.5 1.0
SD B:MET1251 4.5 0.6 1.0
CG B:ARG1250 4.6 0.4 1.0
N B:MET1251 4.6 0.1 1.0
CB B:ALA1254 4.6 0.3 1.0
C B:ALA1218 4.6 0.8 1.0
CA B:ASN1222 4.8 0.5 1.0
C B:LEU1221 4.8 0.0 1.0
CB B:ARG1250 4.8 0.4 1.0
CB B:ASN1222 5.0 0.6 1.0

Gold binding site 4 out of 4 in 2vyf

Go back to Gold Binding Sites List in 2vyf
Gold binding site 4 out of 4 in the Crystal Structure of the Dnac


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Crystal Structure of the Dnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au2427

b:1.0
occ:1.00
O B:MET1249 3.1 1.0 1.0
CG B:MET1249 3.1 1.0 1.0
CE B:MET1249 3.3 1.0 1.0
C B:MET1249 3.6 1.0 1.0
SD B:MET1249 4.0 1.0 1.0
CB B:MET1249 4.1 1.0 1.0
N B:GLN1261 4.3 1.0 1.0
CA B:MET1249 4.3 1.0 1.0
N B:ARG1250 4.3 0.2 1.0
CB B:CYS1253 4.4 1.0 1.0
O B:GLN1261 4.5 1.0 1.0
CA B:GLN1261 4.5 1.0 1.0
CB B:ALA1260 4.5 0.6 1.0
CA B:ARG1250 4.6 0.2 1.0
C B:GLN1261 4.6 1.0 1.0
N B:CYS1253 4.8 1.0 1.0
CA B:CYS1253 4.9 1.0 1.0
C B:ALA1260 5.0 1.0 1.0

Reference:

Y.H.Lo, K.L.Tsai, Y.J.Sun, W.T.Chen, C.Y.Huang, C.D.Hsiao. The Crystal Structure of A Replicative Hexameric Helicase Dnac and Its Complex with Single-Stranded Dna. Nucleic Acids Res. V. 37 804 2009.
ISSN: ISSN 0305-1048
PubMed: 19074952
DOI: 10.1093/NAR/GKN999
Page generated: Sat Dec 12 01:53:20 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy