Copper in the structure of Crystal Structure Of Electron Transfer Complex of Nitrite Reductase With Cytochrome C (pdb 2zon)

The binding sites of Copper atom in the structure of Crystal Structure Of Electron Transfer Complex of Nitrite Reductase With Cytochrome C (pdb code 2zon). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2zon structure was solved by M.NOJIRI, H.KOTEISHI, K.YAMAGUCHI, S.SUZUKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-1.7 Space group P212121 a (A) 63.345 b (A) 103.942 c (A) 163.144 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.2 Rfree (%) 19.5 Copper Binding Sites: Copper binding site 1 out of 6 in 2zon Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2zon. 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: Met56, A: Pro88, A: His89, A: Asn90, A: Cys130, A: Pro132, A: His139, A: Met144, conact list: Atom Atom Distance (A) Cu SD A:Met56 4.34 Cu O A:Pro88 4.17 Cu C A:Pro88 4.92 Cu NE2 A:His89 4.16 Cu N A:His89 4.86 Cu CB A:His89 3.46 Cu ND1 A:His89 2.09 Cu CD2 A:His89 4.23 Cu C A:His89 4.87 Cu CE1 A:His89 3.02 Cu CG A:His89 3.12 Cu CA A:His89 3.85 Cu N A:Asn90 4.72 Cu CB A:Cys130 3.14 Cu SG A:Cys130 2.20 Cu CA A:Cys130 4.56 Cu CD A:Pro132 4.42 Cu CG A:Pro132 3.97 Cu NE2 A:His139 4.15 Cu CB A:His139 3.49 Cu ND1 A:His139 2.10 Cu CD2 A:His139 4.22 Cu CE1 A:His139 3.02 Cu CG A:His139 3.13 Cu CA A:His139 4.70 Cu CB A:Met144 4.57 Cu CE A:Met144 3.33 Cu CG A:Met144 4.10 Cu SD A:Met144 2.56 interactive model: Copper binding site 2 out of 6 in 2zon Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2zon. 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: Asp92, A: His94, A: His129, B: His249, B: His300, A: Hoh622, A: Hoh695, conact list: Atom Atom Distance (A) Cu OD2 A:Asp92 3.78 Cu OD1 A:Asp92 4.71 Cu CG A:Asp92 4.42 Cu NE2 A:His94 2.08 Cu ND1 A:His94 4.12 Cu CD2 A:His94 3.18 Cu CE1 A:His94 2.94 Cu CG A:His94 4.26 Cu NE2 A:His129 2.05 Cu ND1 A:His129 4.17 Cu CD2 A:His129 2.94 Cu CE1 A:His129 3.11 Cu CG A:His129 4.13 Cu NE2 B:His249 3.89 Cu ND1 B:His249 4.94 Cu CD2 B:His249 4.34 Cu CE1 B:His249 4.34 Cu CG B:His249 4.98 Cu NE2 B:His300 2.00 Cu ND1 B:His300 4.09 Cu CD2 B:His300 3.01 Cu CE1 B:His300 2.98 Cu CG B:His300 4.14 Cu O A:Hoh622 2.11 Cu O A:Hoh695 4.39 interactive model: Copper binding site 3 out of 6 in 2zon Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2zon. 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: Met56, B: Pro88, B: His89, B: Asn90, B: Cys130, B: Pro132, B: His139, B: Met144, conact list: Atom Atom Distance (A) Cu SD B:Met56 4.56 Cu O B:Pro88 4.11 Cu C B:Pro88 4.87 Cu NE2 B:His89 4.19 Cu N B:His89 4.81 Cu CB B:His89 3.49 Cu ND1 B:His89 2.11 Cu CD2 B:His89 4.26 Cu C B:His89 4.83 Cu CE1 B:His89 3.04 Cu CG B:His89 3.15 Cu CA B:His89 3.81 Cu N B:Asn90 4.70 Cu CB B:Cys130 3.13 Cu SG B:Cys130 2.20 Cu CA B:Cys130 4.54 Cu CD B:Pro132 4.29 Cu CG B:Pro132 3.87 Cu NE2 B:His139 4.12 Cu CB B:His139 3.49 Cu ND1 B:His139 2.07 Cu CD2 B:His139 4.20 Cu CE1 B:His139 2.98 Cu CG B:His139 3.11 Cu CA B:His139 4.72 Cu CB B:Met144 4.62 Cu CE B:Met144 3.44 Cu CG B:Met144 4.13 Cu SD B:Met144 2.63 interactive model: Copper binding site 4 out of 6 in 2zon Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2zon. 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: Asp92, B: His94, B: His129, C: His249, C: His300, B: Hoh528, B: Hoh744, conact list: Atom Atom Distance (A) Cu OD2 B:Asp92 3.73 Cu OD1 B:Asp92 4.72 Cu CG B:Asp92 4.41 Cu NE2 B:His94 2.04 Cu ND1 B:His94 4.06 Cu CD2 B:His94 3.18 Cu CE1 B:His94 2.87 Cu CG B:His94 4.23 Cu NE2 B:His129 2.04 Cu ND1 B:His129 4.16 Cu CD2 B:His129 2.93 Cu CE1 B:His129 3.10 Cu CG B:His129 4.12 Cu NE2 C:His249 3.92 Cu ND1 C:His249 4.88 Cu CD2 C:His249 4.37 Cu CE1 C:His249 4.30 Cu CG C:His249 4.96 Cu NE2 C:His300 2.07 Cu ND1 C:His300 4.15 Cu CD2 C:His300 3.09 Cu CE1 C:His300 3.02 Cu CG C:His300 4.21 Cu O B:Hoh528 2.15 Cu O B:Hoh744 4.98 interactive model: Copper binding site 5 out of 6 in 2zon Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 2zon. 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: Met56, C: Pro88, C: His89, C: Asn90, C: Cys130, C: Pro132, C: His139, C: Met144, conact list: Atom Atom Distance (A) Cu SD C:Met56 4.48 Cu O C:Pro88 4.12 Cu C C:Pro88 4.87 Cu NE2 C:His89 4.26 Cu N C:His89 4.83 Cu CB C:His89 3.53 Cu ND1 C:His89 2.19 Cu CD2 C:His89 4.33 Cu C C:His89 4.86 Cu CE1 C:His89 3.12 Cu CG C:His89 3.21 Cu CA C:His89 3.84 Cu N C:Asn90 4.71 Cu CB C:Cys130 3.15 Cu SG C:Cys130 2.17 Cu CA C:Cys130 4.56 Cu CD C:Pro132 4.34 Cu CG C:Pro132 3.90 Cu NE2 C:His139 4.19 Cu CB C:His139 3.57 Cu ND1 C:His139 2.15 Cu CD2 C:His139 4.28 Cu CE1 C:His139 3.05 Cu CG C:His139 3.20 Cu CA C:His139 4.75 Cu CB C:Met144 4.61 Cu CE C:Met144 3.40 Cu CG C:Met144 4.15 Cu SD C:Met144 2.64 interactive model: Copper binding site 6 out of 6 in 2zon Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 2zon. 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: His249, A: His300, C: Asp92, C: His94, C: His129, C: Hoh819, C: Hoh1003, conact list: Atom Atom Distance (A) Cu NE2 A:His249 4.06 Cu ND1 A:His249 4.88 Cu CD2 A:His249 4.50 Cu CE1 A:His249 4.34 Cu NE2 A:His300 2.04 Cu ND1 A:His300 4.11 Cu CD2 A:His300 3.07 Cu CE1 A:His300 2.98 Cu CG A:His300 4.19 Cu OD2 C:Asp92 3.72 Cu OD1 C:Asp92 4.73 Cu CG C:Asp92 4.40 Cu NE2 C:His94 2.02 Cu ND1 C:His94 4.06 Cu CD2 C:His94 3.12 Cu CE1 C:His94 2.90 Cu CG C:His94 4.20 Cu NE2 C:His129 2.07 Cu ND1 C:His129 4.19 Cu CD2 C:His129 2.95 Cu CE1 C:His129 3.14 Cu CG C:His129 4.14 Cu O C:Hoh819 2.10 Cu O C:Hoh1003 4.41 interactive model: