Gold in PDB 2vyf: Crystal Structure of the Dnac

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

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 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 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 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 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

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