Copper in the structure of Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes (pdb 2avf)

The binding sites of Copper atom in the structure of Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes (pdb code 2avf). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2avf structure was solved by H.T.LI, T.CHANG, W.C.CHANG, C.J.CHEN, M.Y.LIU, L.L.GUI, J.P.ZHANG, X.M.AN, W.R.CHANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.6 Space group P1211 a (A) 85.783 b (A) 111.072 c (A) 122.884 alpha (°) 90.00 beta (°) 101.67 gamma (°) 90.00 Rfactor (%) 18.2 Rfree (%) 21.7 Copper Binding Sites: Copper binding site 1 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp98, A: His100, A: His135, B: His255, B: His306, B: Leu308, B: Cl601, conact list: Atom Atom Distance (A) Cu OD1 A:Asp98 4.75 Cu CG A:Asp98 4.94 Cu NE2 A:His100 2.06 Cu ND1 A:His100 4.08 Cu CD2 A:His100 3.19 Cu CE1 A:His100 2.90 Cu CG A:His100 4.24 Cu NE2 A:His135 2.06 Cu ND1 A:His135 4.11 Cu CD2 A:His135 3.14 Cu CE1 A:His135 2.95 Cu CG A:His135 4.23 Cu NE2 B:His255 3.99 Cu ND1 B:His255 4.97 Cu CD2 B:His255 4.14 Cu CE1 B:His255 4.54 Cu CG B:His255 4.77 Cu NE2 B:His306 1.98 Cu ND1 B:His306 4.03 Cu CD2 B:His306 3.06 Cu CE1 B:His306 2.87 Cu CG B:His306 4.15 Cu CD2 B:Leu308 4.83 Cu CL B:Cl601 2.16 interactive model: Copper binding site 2 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Met62, A: Leu94, A: His95, A: Asn96, A: Cys136, A: Pro138, A: His145, A: Met150, conact list: Atom Atom Distance (A) Cu CB A:Met62 4.86 Cu SD A:Met62 4.64 Cu O A:Leu94 4.46 Cu NE2 A:His95 4.25 Cu CB A:His95 3.53 Cu ND1 A:His95 2.19 Cu CD2 A:His95 4.31 Cu CE1 A:His95 3.12 Cu CG A:His95 3.19 Cu CA A:His95 4.04 Cu N A:Asn96 4.85 Cu CB A:Cys136 3.19 Cu SG A:Cys136 2.34 Cu CA A:Cys136 4.63 Cu CD A:Pro138 4.72 Cu CG A:Pro138 4.81 Cu NE2 A:His145 4.17 Cu CB A:His145 3.58 Cu ND1 A:His145 2.13 Cu CD2 A:His145 4.28 Cu CE1 A:His145 3.02 Cu CG A:His145 3.19 Cu CA A:His145 4.84 Cu CB A:Met150 4.24 Cu CE A:Met150 3.14 Cu CG A:Met150 3.90 Cu SD A:Met150 2.35 interactive model: Copper binding site 3 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His100, B: His135, C: His255, C: His306, B: Cl602, conact list: Atom Atom Distance (A) Cu NE2 B:His100 2.08 Cu ND1 B:His100 4.08 Cu CD2 B:His100 3.22 Cu CE1 B:His100 2.89 Cu CG B:His100 4.26 Cu NE2 B:His135 2.23 Cu ND1 B:His135 4.34 Cu CD2 B:His135 3.16 Cu CE1 B:His135 3.24 Cu CG B:His135 4.33 Cu NE2 C:His255 4.16 Cu ND1 C:His255 4.86 Cu CD2 C:His255 4.35 Cu CE1 C:His255 4.50 Cu CG C:His255 4.80 Cu NE2 C:His306 2.23 Cu ND1 C:His306 4.29 Cu CD2 C:His306 3.26 Cu CE1 C:His306 3.14 Cu CG C:His306 4.38 Cu CL B:Cl602 2.21 interactive model: Copper binding site 4 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Met62, B: Leu94, B: His95, B: Asn96, B: Cys136, B: Pro138, B: His145, B: Met150, conact list: Atom Atom Distance (A) Cu CB B:Met62 4.84 Cu SD B:Met62 4.48 Cu O B:Leu94 4.27 Cu NE2 B:His95 4.21 Cu CB B:His95 3.68 Cu ND1 B:His95 2.21 Cu CD2 B:His95 4.34 Cu CE1 B:His95 3.06 Cu CG B:His95 3.28 Cu CA B:His95 4.06 Cu N B:Asn96 4.91 Cu CB B:Cys136 3.20 Cu SG B:Cys136 2.39 Cu CA B:Cys136 4.65 Cu CD B:Pro138 4.76 Cu CG B:Pro138 4.80 Cu NE2 B:His145 3.97 Cu CB B:His145 3.54 Cu ND1 B:His145 1.95 Cu CD2 B:His145 4.12 Cu CE1 B:His145 2.80 Cu CG B:His145 3.07 Cu CA B:His145 4.78 Cu CB B:Met150 4.16 Cu CE B:Met150 3.14 Cu CG B:Met150 3.80 Cu SD B:Met150 2.26 interactive model: Copper binding site 5 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His255, A: His306, C: Asp98, C: His100, C: His135, C: Cl603, A: Hoh540, conact list: Atom Atom Distance (A) Cu NE2 A:His255 4.03 Cu CD2 A:His255 4.26 Cu CE1 A:His255 4.58 Cu CG A:His255 4.92 Cu NE2 A:His306 2.12 Cu ND1 A:His306 4.18 Cu CD2 A:His306 3.17 Cu CE1 A:His306 3.03 Cu CG A:His306 4.28 Cu OD2 C:Asp98 4.31 Cu OD1 C:Asp98 4.78 Cu CG C:Asp98 4.61 Cu NE2 C:His100 2.06 Cu ND1 C:His100 4.09 Cu CD2 C:His100 3.16 Cu CE1 C:His100 2.91 Cu CG C:His100 4.23 Cu NE2 C:His135 2.05 Cu ND1 C:His135 4.17 Cu CD2 C:His135 2.95 Cu CE1 C:His135 3.11 Cu CG C:His135 4.13 Cu CL C:Cl603 2.17 Cu O A:Hoh540 4.86 interactive model: Copper binding site 6 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Met62, C: Leu94, C: His95, C: Asn96, C: Cys136, C: Pro138, C: His145, C: Met150, conact list: Atom Atom Distance (A) Cu CB C:Met62 4.78 Cu SD C:Met62 4.34 Cu O C:Leu94 4.49 Cu NE2 C:His95 4.25 Cu CB C:His95 3.79 Cu ND1 C:His95 2.27 Cu CD2 C:His95 4.41 Cu CE1 C:His95 3.07 Cu CG C:His95 3.37 Cu CA C:His95 4.11 Cu N C:Asn96 4.86 Cu CB C:Cys136 3.29 Cu SG C:Cys136 2.42 Cu CA C:Cys136 4.75 Cu CD C:Pro138 4.55 Cu CG C:Pro138 3.96 Cu NE2 C:His145 4.13 Cu CB C:His145 3.54 Cu ND1 C:His145 2.08 Cu CD2 C:His145 4.23 Cu CE1 C:His145 2.97 Cu CG C:His145 3.15 Cu CA C:His145 4.74 Cu CB C:Met150 4.21 Cu CE C:Met150 3.39 Cu CG C:Met150 3.85 Cu SD C:Met150 2.33 interactive model: Copper binding site 7 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp98, D: His100, D: His135, E: His255, E: His306, E: Leu308, D: Cl604, conact list: Atom Atom Distance (A) Cu OD2 D:Asp98 4.34 Cu NE2 D:His100 2.23 Cu ND1 D:His100 4.23 Cu CD2 D:His100 3.32 Cu CE1 D:His100 3.06 Cu CG D:His100 4.39 Cu NE2 D:His135 1.97 Cu ND1 D:His135 4.02 Cu CD2 D:His135 3.03 Cu CE1 D:His135 2.88 Cu CG D:His135 4.12 Cu NE2 E:His255 4.40 Cu CD2 E:His255 4.59 Cu CE1 E:His255 4.71 Cu NE2 E:His306 2.02 Cu ND1 E:His306 4.06 Cu CD2 E:His306 3.12 Cu CE1 E:His306 2.90 Cu CG E:His306 4.20 Cu CD1 E:Leu308 4.94 Cu CD2 E:Leu308 4.92 Cu CL D:Cl604 2.05 interactive model: Copper binding site 8 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Met62, D: Leu94, D: His95, D: Asn96, D: Cys136, D: Pro138, D: His145, D: Met150, conact list: Atom Atom Distance (A) Cu CB D:Met62 4.90 Cu SD D:Met62 4.58 Cu O D:Leu94 4.77 Cu NE2 D:His95 4.11 Cu CB D:His95 3.83 Cu ND1 D:His95 2.15 Cu CD2 D:His95 4.33 Cu CE1 D:His95 2.90 Cu CG D:His95 3.32 Cu CA D:His95 4.25 Cu N D:Asn96 4.93 Cu CB D:Cys136 3.07 Cu SG D:Cys136 2.23 Cu CA D:Cys136 4.52 Cu CD D:Pro138 4.61 Cu CG D:Pro138 4.59 Cu NE2 D:His145 4.41 Cu CB D:His145 3.72 Cu ND1 D:His145 2.36 Cu CD2 D:His145 4.50 Cu CE1 D:His145 3.25 Cu CG D:His145 3.40 Cu CA D:His145 4.92 Cu CB D:Met150 4.11 Cu CE D:Met150 3.05 Cu CG D:Met150 3.79 Cu SD D:Met150 2.25 interactive model: Copper binding site 9 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Asp98, E: His100, E: His135, F: His255, F: His306, F: Cl605, F: Hoh614, conact list: Atom Atom Distance (A) Cu OD1 E:Asp98 4.64 Cu CG E:Asp98 4.90 Cu NE2 E:His100 1.85 Cu ND1 E:His100 3.85 Cu CD2 E:His100 3.01 Cu CE1 E:His100 2.66 Cu CG E:His100 4.04 Cu NE2 E:His135 2.17 Cu ND1 E:His135 4.24 Cu CD2 E:His135 3.19 Cu CE1 E:His135 3.10 Cu CG E:His135 4.32 Cu NE2 F:His255 4.13 Cu ND1 F:His255 4.92 Cu CD2 F:His255 4.27 Cu CE1 F:His255 4.56 Cu CG F:His255 4.78 Cu NE2 F:His306 2.05 Cu ND1 F:His306 4.11 Cu CD2 F:His306 3.05 Cu CE1 F:His306 3.00 Cu CG F:His306 4.17 Cu CL F:Cl605 2.06 Cu O F:Hoh614 4.96 interactive model: Copper binding site 10 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Met62, E: Leu94, E: His95, E: Asn96, E: Cys136, E: Pro138, E: His145, E: Met150, conact list: Atom Atom Distance (A) Cu CB E:Met62 4.78 Cu SD E:Met62 4.39 Cu O E:Leu94 4.32 Cu NE2 E:His95 4.22 Cu CB E:His95 3.83 Cu ND1 E:His95 2.23 Cu CD2 E:His95 4.41 Cu CE1 E:His95 3.01 Cu CG E:His95 3.37 Cu CA E:His95 4.15 Cu N E:Asn96 4.95 Cu CB E:Cys136 3.25 Cu SG E:Cys136 2.40 Cu CA E:Cys136 4.70 Cu CD E:Pro138 4.75 Cu CG E:Pro138 4.70 Cu NE2 E:His145 4.04 Cu CB E:His145 3.48 Cu ND1 E:His145 2.04 Cu CD2 E:His145 4.13 Cu CE1 E:His145 2.92 Cu CG E:His145 3.07 Cu CA E:His145 4.73 Cu CB E:Met150 4.24 Cu CE E:Met150 3.31 Cu CG E:Met150 3.88 Cu SD E:Met150 2.33 interactive model: Copper binding site 11 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His255, D: His306, F: Asp98, F: His100, F: His135, F: Cl606, D: Hoh607, conact list: Atom Atom Distance (A) Cu NE2 D:His255 4.11 Cu ND1 D:His255 4.93 Cu CD2 D:His255 4.36 Cu CE1 D:His255 4.50 Cu CG D:His255 4.87 Cu NE2 D:His306 2.15 Cu ND1 D:His306 4.22 Cu CD2 D:His306 3.17 Cu CE1 D:His306 3.08 Cu CG D:His306 4.29 Cu OD2 F:Asp98 3.98 Cu CG F:Asp98 4.77 Cu NE2 F:His100 1.99 Cu ND1 F:His100 3.94 Cu CD2 F:His100 3.18 Cu CE1 F:His100 2.73 Cu CG F:His100 4.18 Cu NE2 F:His135 2.08 Cu ND1 F:His135 4.17 Cu CD2 F:His135 3.09 Cu CE1 F:His135 3.04 Cu CG F:His135 4.22 Cu CL F:Cl606 2.14 Cu O D:Hoh607 4.88 interactive model: Copper binding site 12 out of 12 in 2avf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Copper in the PDB 2avf. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: Met62, F: Leu94, F: His95, F: Cys136, F: Pro138, F: His145, F: Met150, conact list: Atom Atom Distance (A) Cu CB F:Met62 4.84 Cu SD F:Met62 4.58 Cu O F:Leu94 4.59 Cu NE2 F:His95 4.15 Cu CB F:His95 3.84 Cu ND1 F:His95 2.23 Cu CD2 F:His95 4.35 Cu CE1 F:His95 2.97 Cu CG F:His95 3.35 Cu CA F:His95 4.25 Cu CB F:Cys136 3.30 Cu SG F:Cys136 2.46 Cu CA F:Cys136 4.77 Cu CD F:Pro138 4.84 Cu CG F:Pro138 4.83 Cu NE2 F:His145 3.90 Cu CB F:His145 3.57 Cu ND1 F:His145 1.93 Cu CD2 F:His145 4.06 Cu CE1 F:His145 2.73 Cu CG F:His145 3.05 Cu CA F:His145 4.79 Cu CB F:Met150 4.26 Cu CE F:Met150 3.49 Cu CG F:Met150 3.92 Cu SD F:Met150 2.42 interactive model: