Gold in the structure of Time-Dependent and Protein-Directed In Situ Growth Of Gold Nanoparticles in A Single Crystal of Lysozyme (pdb 3p64)

The binding sites of Gold atom in the structure of Time-Dependent and Protein-Directed In Situ Growth Of Gold Nanoparticles in A Single Crystal of Lysozyme (pdb code 3p64). This binding sites where shown with 5.0 Angstroms radius around Gold atom. The 3p64 structure was solved by H.WEI, Z.WANG, J.ZHANG, S.HOUSE, Y.-G.GAO, L.YANG, H.ROBINSON, L.H.TAN, H.XING, C.HOU, I.M.ROBERTSON, J.-M.ZUO, Y.LU, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.3 Space group P43212 a (A) 78.567 b (A) 78.567 c (A) 36.947 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 23.4 Gold Binding Sites: Gold binding site 1 out of 4 in 3p64 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Gold in the PDB 3p64. 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: Asn65, A: Asp66, A: Gly67, A: Arg68, A: Thr69, A: Pro70, A: Ser72, A: Hoh2006, A: Hoh2023, A: Hoh2041, A: Hoh2061, A: Hoh2107, A: Hoh2150, A: Hoh2157, A: Hoh2227, conact list: Atom Atom Distance (A) Au OD1 A:Asn65 3.63 Au CG A:Asn65 4.80 Au N A:Asp66 4.86 Au C A:Asp66 4.73 Au OD1 A:Asp66 4.24 Au O A:Gly67 4.13 Au N A:Gly67 3.66 Au C A:Gly67 3.47 Au CA A:Gly67 3.49 Au N A:Arg68 3.43 Au C A:Arg68 4.21 Au CA A:Arg68 4.28 Au O A:Thr69 3.35 Au N A:Thr69 3.19 Au CB A:Thr69 4.14 Au OG1 A:Thr69 4.73 Au C A:Thr69 3.62 Au CA A:Thr69 3.82 Au N A:Pro70 4.41 Au CA A:Pro70 4.98 Au CB A:Ser72 4.84 Au OG A:Ser72 3.71 Au O A:Hoh2006 3.07 Au O A:Hoh2023 4.86 Au O A:Hoh2041 3.94 Au O A:Hoh2061 3.06 Au O A:Hoh2107 3.53 Au O A:Hoh2150 4.61 Au O A:Hoh2157 3.05 Au O A:Hoh2227 4.67 interactive model: Gold binding site 2 out of 4 in 3p64 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Gold in the PDB 3p64. 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: Arg21, A: Tyr23, A: Gly104, A: Hoh2008, conact list: Atom Atom Distance (A) Au O A:Arg21 4.67 Au CE2 A:Tyr23 3.69 Au CD2 A:Tyr23 4.92 Au CZ A:Tyr23 3.70 Au CE1 A:Tyr23 4.90 Au OH A:Tyr23 3.02 Au N A:Gly104 4.67 Au CA A:Gly104 4.08 Au O A:Hoh2008 3.34 interactive model: Gold binding site 3 out of 4 in 3p64 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Gold in the PDB 3p64. 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: Ala11, A: Arg14, A: His15, A: Asp87, A: Ile88, A: Thr89, A: Cl1319, A: Hoh2081, A: Hoh2116, conact list: Atom Atom Distance (A) Au O A:Ala11 4.83 Au CB A:Ala11 4.47 Au NH1 A:Arg14 4.21 Au NE2 A:His15 2.01 Au ND1 A:His15 3.94 Au CD2 A:His15 2.94 Au CE1 A:His15 2.90 Au CG A:His15 4.00 Au CB A:Asp87 4.75 Au OD2 A:Asp87 4.14 Au C A:Asp87 4.49 Au OD1 A:Asp87 3.49 Au CG A:Asp87 3.90 Au CA A:Asp87 4.47 Au N A:Ile88 3.71 Au CB A:Ile88 4.58 Au CD1 A:Ile88 4.73 Au C A:Ile88 4.68 Au CG1 A:Ile88 3.67 Au CA A:Ile88 4.51 Au N A:Thr89 4.29 Au OG1 A:Thr89 4.20 Au CL A:Cl1319 1.80 Au O A:Hoh2081 4.89 Au O A:Hoh2116 3.32 interactive model: Gold binding site 4 out of 4 in 3p64 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Gold in the PDB 3p64. 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: Ser24, A: Leu25, A: Gly26, A: Asn27, A: Val120, A: Gln121, A: Ile124, A: Hoh2110, conact list: Atom Atom Distance (A) Au O A:Ser24 4.99 Au CB A:Ser24 3.54 Au OG A:Ser24 2.88 Au C A:Ser24 4.46 Au CA A:Ser24 4.62 Au N A:Leu25 4.32 Au C A:Leu25 4.46 Au CA A:Leu25 4.87 Au N A:Gly26 3.28 Au C A:Gly26 4.59 Au CA A:Gly26 3.61 Au N A:Asn27 4.68 Au O A:Val120 4.28 Au CG2 A:Val120 4.21 Au C A:Val120 4.27 Au O A:Gln121 5.00 Au N A:Gln121 3.96 Au CB A:Gln121 3.91 Au C A:Gln121 4.81 Au CG A:Gln121 4.03 Au CA A:Gln121 3.58 Au CD1 A:Ile124 4.13 Au CG1 A:Ile124 4.29 Au O A:Hoh2110 4.87 interactive model: