Gold in the structure of Time-Dependent and Protein-Directed In Situ Growth Of Gold Nanoparticles in A Single Crystal of Lysozyme (pdb 3p68)

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 3p68). This binding sites where shown with 5.0 Angstroms radius around Gold atom. The 3p68 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) 10.0-1.6 Space group P43212 a (A) 78.400 b (A) 78.400 c (A) 37.224 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.7 Rfree (%) 25.5 Gold Binding Sites: Gold binding site 1 out of 7 in 3p68 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Gold in the PDB 3p68. 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 4.67 Au CE2 A:Tyr23 3.76 Au CD2 A:Tyr23 4.98 Au CZ A:Tyr23 3.77 Au CE1 A:Tyr23 4.99 Au OH A:Tyr23 3.04 Au N A:Gly104 4.80 Au CA A:Gly104 4.19 Au O A:Hoh2007 3.36 interactive model: Gold binding site 2 out of 7 in 3p68 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Gold in the PDB 3p68. 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: Au31307, A: Hoh2005, A: Hoh2015, A: Hoh2027, A: Hoh2033, A: Hoh2092, conact list: Atom Atom Distance (A) Au OD1 A:Asn65 3.70 Au CG A:Asn65 4.91 Au C A:Asp66 4.89 Au OD1 A:Asp66 4.40 Au O A:Gly67 4.11 Au N A:Gly67 3.78 Au C A:Gly67 3.56 Au CA A:Gly67 3.68 Au N A:Arg68 3.58 Au C A:Arg68 4.36 Au CA A:Arg68 4.42 Au O A:Thr69 3.43 Au N A:Thr69 3.33 Au CB A:Thr69 4.29 Au OG1 A:Thr69 4.92 Au C A:Thr69 3.71 Au CA A:Thr69 3.95 Au N A:Pro70 4.44 Au CA A:Pro70 4.94 Au CB A:Ser72 4.68 Au OG A:Ser72 3.55 Au AU A:Au31307 4.75 Au O A:Hoh2005 3.91 Au O A:Hoh2015 3.19 Au O A:Hoh2027 3.31 Au O A:Hoh2033 4.79 Au O A:Hoh2092 3.05 interactive model: Gold binding site 3 out of 7 in 3p68 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Gold in the PDB 3p68. 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: Hoh2027, A: Hoh2076, A: Hoh2095, conact list: Atom Atom Distance (A) Au ND2 A:Asn65 3.02 Au OD1 A:Asn65 4.23 Au CG A:Asn65 4.06 Au O A:Asp66 4.94 Au C A:Asp66 4.67 Au N A:Gly67 4.05 Au CA A:Gly67 3.73 Au O A:Hoh2027 4.60 Au O A:Hoh2076 3.46 Au O A:Hoh2095 4.86 interactive model: Gold binding site 4 out of 7 in 3p68 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Gold in the PDB 3p68. 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 4.98 Au CB A:Ser24 3.61 Au OG A:Ser24 3.07 Au C A:Ser24 4.49 Au CA A:Ser24 4.72 Au N A:Leu25 4.24 Au C A:Leu25 4.39 Au CA A:Leu25 4.77 Au N A:Gly26 3.23 Au C A:Gly26 4.60 Au CA A:Gly26 3.56 Au N A:Asn27 4.76 Au O A:Val120 4.38 Au CG2 A:Val120 4.52 Au C A:Val120 4.42 Au N A:Gln121 4.06 Au CB A:Gln121 4.08 Au C A:Gln121 4.81 Au CG A:Gln121 4.08 Au CA A:Gln121 3.66 Au CD1 A:Ile124 3.58 Au CG1 A:Ile124 4.00 interactive model: Gold binding site 5 out of 7 in 3p68 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Gold in the PDB 3p68. 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: Arg45, A: Gly49, A: Ser50, A: Thr51, A: Tyr53, A: Ser60, A: Asp66, A: Arg68, A: Thr69, conact list: Atom Atom Distance (A) Au CD A:Arg45 4.59 Au CZ A:Arg45 4.12 Au NE A:Arg45 3.83 Au NH2 A:Arg45 4.06 Au O A:Gly49 2.79 Au C A:Gly49 3.83 Au O A:Ser50 4.09 Au N A:Ser50 4.21 Au CB A:Ser50 4.84 Au C A:Ser50 3.46 Au CA A:Ser50 3.61 Au N A:Thr51 3.31 Au CB A:Thr51 3.45 Au CG2 A:Thr51 4.78 Au OG1 A:Thr51 2.73 Au CA A:Thr51 3.99 Au OH A:Tyr53 4.32 Au CB A:Ser60 4.66 Au OG A:Ser60 3.70 Au CB A:Asp66 4.99 Au OD2 A:Asp66 2.77 Au OD1 A:Asp66 3.84 Au CG A:Asp66 3.66 Au O A:Arg68 3.79 Au CB A:Arg68 4.63 Au CD A:Arg68 3.73 Au CZ A:Arg68 3.94 Au C A:Arg68 4.24 Au CG A:Arg68 3.56 Au NE A:Arg68 2.96 Au NH2 A:Arg68 4.11 Au CA A:Arg68 4.96 Au N A:Thr69 4.68 Au CB A:Thr69 4.34 Au CG2 A:Thr69 4.80 Au OG1 A:Thr69 3.04 Au CA A:Thr69 4.76 interactive model: Gold binding site 6 out of 7 in 3p68 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Gold in the PDB 3p68. 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: Asn74, A: Ile78, A: Pro79, A: Hoh2076, A: Hoh2089, A: Hoh2095, A: Hoh2113, conact list: Atom Atom Distance (A) Au O A:Asn65 4.37 Au CB A:Asn65 3.89 Au ND2 A:Asn65 3.28 Au C A:Asn65 4.98 Au CG A:Asn65 4.06 Au CA A:Asn65 4.98 Au ND2 A:Asn74 4.82 Au O A:Ile78 4.79 Au C A:Ile78 4.54 Au N A:Pro79 4.00 Au CB A:Pro79 3.83 Au CD A:Pro79 4.25 Au CG A:Pro79 4.47 Au CA A:Pro79 3.83 Au O A:Hoh2076 4.96 Au O A:Hoh2089 3.22 Au O A:Hoh2095 3.11 Au O A:Hoh2113 4.91 interactive model: Gold binding site 7 out of 7 in 3p68 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Gold in the PDB 3p68. 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: Au31302, A: Hoh2005, A: Hoh2015, conact list: Atom Atom Distance (A) Au O A:Ser60 2.39 Au CB A:Ser60 4.26 Au C A:Ser60 3.54 Au CA A:Ser60 4.10 Au O A:Arg61 4.55 Au N A:Arg61 4.65 Au C A:Arg61 4.54 Au CA A:Arg61 4.87 Au N A:Trp62 4.82 Au O A:Cys64 2.32 Au N A:Cys64 4.30 Au C A:Cys64 3.39 Au CA A:Cys64 4.50 Au N A:Asn65 4.08 Au CB A:Asn65 4.77 Au C A:Asn65 4.81 Au OD1 A:Asn65 4.75 Au CA A:Asn65 3.87 Au N A:Asp66 4.64 Au CB A:Thr69 4.85 Au O A:Ser72 4.70 Au CB A:Ser72 3.34 Au OG A:Ser72 2.53 Au C A:Ser72 4.17 Au CA A:Ser72 4.40 Au O A:Arg73 2.33 Au N A:Arg73 3.97 Au C A:Arg73 3.43 Au CA A:Arg73 4.29 Au N A:Asn74 4.32 Au CB A:Asn74 4.72 Au CA A:Asn74 4.49 Au AU A:Au31302 4.75 Au O A:Hoh2005 2.45 Au O A:Hoh2015 2.53 interactive model: