Gold in the structure of Crystal Structure of the Dnac (pdb 2vyf)

The binding sites of Gold atom in the structure of Crystal Structure of the Dnac (pdb code 2vyf). This binding sites where shown with 5.0 Angstroms radius around Gold atom. The 2vyf structure was solved by Y.H.LO, K.L.TSAI, Y.J.SUN, C.D.HSIAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.9-3.6 Space group P63 a (A) 176.968 b (A) 176.968 c (A) 108.824 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 29.3 Rfree (%) 32.4 Gold Binding Sites: Gold binding site 1 out of 4 in 2vyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Gold in the PDB 2vyf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ala218, A: Leu221, A: Asn222, A: Arg250, A: Met251, A: Ala254, A: Glu434, conact list: Atom Atom Distance (A) Au O A:Ala218 3.97 Au N A:Ala218 4.88 Au C A:Ala218 4.31 Au CB A:Ala218 3.86 Au CA A:Ala218 3.72 Au CB A:Leu221 4.68 Au CD1 A:Leu221 2.80 Au CD2 A:Leu221 3.13 Au CG A:Leu221 3.17 Au ND2 A:Asn222 3.58 Au OD1 A:Asn222 4.97 Au CG A:Asn222 4.61 Au O A:Arg250 3.90 Au C A:Arg250 4.38 Au N A:Met251 4.61 Au CA A:Met251 4.38 Au CB A:Ala254 3.73 Au O A:Glu434 4.18 interactive model: Gold binding site 2 out of 4 in 2vyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Gold in the PDB 2vyf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Met249, A: Arg250, A: Cys253, conact list: Atom Atom Distance (A) Au O A:Met249 2.99 Au CB A:Met249 3.90 Au CE A:Met249 3.17 Au C A:Met249 3.51 Au CG A:Met249 2.82 Au SD A:Met249 3.19 Au CA A:Met249 4.22 Au N A:Arg250 4.13 Au CD A:Arg250 4.47 Au CZ A:Arg250 2.94 Au C A:Arg250 4.99 Au NE A:Arg250 3.72 Au NH2 A:Arg250 2.88 Au NH1 A:Arg250 3.00 Au CA A:Arg250 4.32 Au N A:Cys253 4.21 Au CB A:Cys253 3.34 Au SG A:Cys253 4.31 Au CA A:Cys253 4.37 interactive model: Gold binding site 3 out of 4 in 2vyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Gold in the PDB 2vyf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Ala1218, B: Leu1221, B: Asn1222, B: Arg1250, B: Met1251, B: Ala1254, conact list: Atom Atom Distance (A) Au O B:Ala1218 4.19 Au C B:Ala1218 4.62 Au CB B:Ala1218 4.42 Au CA B:Ala1218 4.09 Au CB B:Leu1221 4.42 Au CD1 B:Leu1221 3.36 Au CD2 B:Leu1221 3.74 Au C B:Leu1221 4.80 Au CG B:Leu1221 3.15 Au N B:Asn1222 4.43 Au CB B:Asn1222 4.96 Au CA B:Asn1222 4.77 Au O B:Arg1250 3.76 Au CB B:Arg1250 4.83 Au C B:Arg1250 4.28 Au CG B:Arg1250 4.57 Au N B:Met1251 4.57 Au SD B:Met1251 4.47 Au CA B:Met1251 4.40 Au CB B:Ala1254 4.59 interactive model: Gold binding site 4 out of 4 in 2vyf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Gold in the PDB 2vyf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Gold atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Met1249, B: Arg1250, B: Cys1253, B: Ala1260, B: Gln1261, conact list: Atom Atom Distance (A) Au O B:Met1249 3.06 Au CB B:Met1249 4.09 Au CE B:Met1249 3.34 Au C B:Met1249 3.65 Au CG B:Met1249 3.12 Au SD B:Met1249 3.95 Au CA B:Met1249 4.34 Au N B:Arg1250 4.35 Au CA B:Arg1250 4.57 Au N B:Cys1253 4.81 Au CB B:Cys1253 4.38 Au CA B:Cys1253 4.95 Au C B:Ala1260 4.98 Au CB B:Ala1260 4.53 Au O B:Gln1261 4.48 Au N B:Gln1261 4.30 Au C B:Gln1261 4.64 Au CA B:Gln1261 4.51 interactive model: