Gold in the structure of Time-Dependent and Protein-Directed In Situ Growth Of Gold Nanoparticles in A Single Crystal of Lysozyme (pdb 3p65)

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 3p65). This binding sites where shown with 5.0 Angstroms radius around Gold atom. The 3p65 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) 10.0-2.1 Space group P43212 a (A) 78.641 b (A) 78.641 c (A) 37.130 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.4 Rfree (%) 22.5 Gold Binding Sites: Gold binding site 1 out of 5 in 3p65 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Gold in the PDB 3p65. 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: Hoh2007, conact list: Atom Atom Distance (A) Au O A:Arg21 4.59 Au CE2 A:Tyr23 3.60 Au CD2 A:Tyr23 4.82 Au CZ A:Tyr23 3.63 Au CE1 A:Tyr23 4.83 Au OH A:Tyr23 2.97 Au N A:Gly104 4.69 Au CA A:Gly104 4.11 Au O A:Hoh2007 3.29 interactive model: Gold binding site 2 out of 5 in 3p65 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Gold in the PDB 3p65. 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: Au3310, A: Hoh2005, A: Hoh2026, A: Hoh2038, A: Hoh2058, A: Hoh2076, A: Hoh2080, A: Hoh2151, conact list: Atom Atom Distance (A) Au OD1 A:Asn65 3.66 Au CG A:Asn65 4.84 Au N A:Asp66 4.90 Au C A:Asp66 4.76 Au OD1 A:Asp66 4.26 Au O A:Gly67 4.14 Au N A:Gly67 3.64 Au C A:Gly67 3.49 Au CA A:Gly67 3.54 Au N A:Arg68 3.49 Au C A:Arg68 4.22 Au CA A:Arg68 4.32 Au O A:Thr69 3.38 Au N A:Thr69 3.18 Au CB A:Thr69 4.19 Au OG1 A:Thr69 4.78 Au C A:Thr69 3.63 Au CA A:Thr69 3.82 Au N A:Pro70 4.42 Au CA A:Pro70 4.92 Au CB A:Ser72 4.87 Au OG A:Ser72 3.68 Au AU A:Au3310 4.62 Au O A:Hoh2005 3.13 Au O A:Hoh2026 3.92 Au O A:Hoh2038 4.88 Au O A:Hoh2058 3.18 Au O A:Hoh2076 3.41 Au O A:Hoh2080 3.40 Au O A:Hoh2151 3.98 interactive model: Gold binding site 3 out of 5 in 3p65 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Gold in the PDB 3p65. 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, conact list: Atom Atom Distance (A) Au O A:Ser24 4.91 Au CB A:Ser24 3.43 Au OG A:Ser24 2.99 Au C A:Ser24 4.42 Au CA A:Ser24 4.57 Au N A:Leu25 4.32 Au C A:Leu25 4.38 Au CA A:Leu25 4.84 Au N A:Gly26 3.23 Au C A:Gly26 4.54 Au CA A:Gly26 3.54 Au N A:Asn27 4.62 Au O A:Val120 4.33 Au CG2 A:Val120 4.24 Au C A:Val120 4.35 Au N A:Gln121 4.04 Au CB A:Gln121 3.97 Au C A:Gln121 4.86 Au CG A:Gln121 4.24 Au CA A:Gln121 3.63 Au CD1 A:Ile124 4.01 Au CG1 A:Ile124 4.27 interactive model: Gold binding site 4 out of 5 in 3p65 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Gold in the PDB 3p65. 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: His15, A: Asp87, A: Ile88, A: Thr89, A: Cl305, conact list: Atom Atom Distance (A) Au O A:Ala11 4.65 Au CB A:Ala11 4.32 Au CA A:Ala11 4.90 Au NE2 A:His15 1.95 Au ND1 A:His15 3.93 Au CD2 A:His15 2.87 Au CE1 A:His15 2.88 Au CG A:His15 3.95 Au C A:Asp87 4.75 Au OD1 A:Asp87 3.85 Au CG A:Asp87 4.52 Au CA A:Asp87 4.78 Au N A:Ile88 3.86 Au CB A:Ile88 4.65 Au CD1 A:Ile88 4.56 Au C A:Ile88 4.84 Au CG1 A:Ile88 3.61 Au CA A:Ile88 4.66 Au N A:Thr89 4.52 Au OG1 A:Thr89 4.38 Au CL A:Cl305 1.99 interactive model: Gold binding site 5 out of 5 in 3p65 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Gold in the PDB 3p65. 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: Ser60, A: Arg61, A: Trp62, A: Cys64, A: Asn65, A: Asp66, A: Thr69, A: Ser72, A: Arg73, A: Asn74, A: Au3302, A: Hoh2005, A: Hoh2026, conact list: Atom Atom Distance (A) Au O A:Ser60 2.23 Au CB A:Ser60 4.14 Au OG A:Ser60 4.95 Au C A:Ser60 3.40 Au CA A:Ser60 3.99 Au O A:Arg61 4.65 Au N A:Arg61 4.48 Au C A:Arg61 4.61 Au CA A:Arg61 4.78 Au N A:Trp62 4.91 Au O A:Cys64 2.37 Au N A:Cys64 4.51 Au C A:Cys64 3.50 Au CA A:Cys64 4.65 Au N A:Asn65 4.17 Au CB A:Asn65 4.83 Au C A:Asn65 4.79 Au OD1 A:Asn65 4.61 Au CA A:Asn65 3.91 Au N A:Asp66 4.58 Au O A:Thr69 4.93 Au CB A:Thr69 4.57 Au OG1 A:Thr69 4.92 Au O A:Ser72 4.64 Au CB A:Ser72 3.34 Au OG A:Ser72 2.50 Au C A:Ser72 4.20 Au CA A:Ser72 4.42 Au O A:Arg73 2.51 Au N A:Arg73 4.05 Au C A:Arg73 3.57 Au CA A:Arg73 4.38 Au N A:Asn74 4.43 Au CB A:Asn74 4.80 Au CA A:Asn74 4.68 Au AU A:Au3302 4.62 Au O A:Hoh2005 2.36 Au O A:Hoh2026 2.46 interactive model: