Copper in the structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State (pdb 1oco)

The binding sites of Copper atom in the structure of Bovine Heart Cytochrome C Oxidase in Carbon Monoxide-Bound State (pdb code 1oco). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1oco structure was solved by T.TSUKIHARA, M.YAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 7.0-2.8 Space group P212121 a (A) 189.100 b (A) 210.500 c (A) 178.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 25.6 Copper Binding Sites: Copper binding site 1 out of 6 in 1oco Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1oco. 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: His240, A: Val243, A: Trp288, A: His290, A: His291, A: Cmo520, conact list: Atom Atom Distance (A) Cu NE2 A:His240 4.29 Cu N A:His240 4.81 Cu CB A:His240 3.38 Cu ND1 A:His240 2.16 Cu CD2 A:His240 4.28 Cu CE1 A:His240 3.17 Cu CG A:His240 3.12 Cu CA A:His240 4.00 Cu CG2 A:Val243 4.80 Cu CA A:Trp288 4.99 Cu O A:Trp288 4.90 Cu NE2 A:His290 2.01 Cu ND1 A:His290 4.16 Cu CD2 A:His290 3.08 Cu CE1 A:His290 2.99 Cu CG A:His290 4.22 Cu NE2 A:His291 1.96 Cu ND1 A:His291 4.12 Cu CD2 A:His291 2.68 Cu CE1 A:His291 3.13 Cu CG A:His291 3.93 Cu O A:Cmo520 2.42 Cu C A:Cmo520 3.66 interactive model: Copper binding site 2 out of 6 in 1oco Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1oco. 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: His102, B: Trp104, B: Leu160, B: His161, B: Cys196, B: Glu198, B: Cys200, B: His204, B: Met207, B: Cu229, conact list: Atom Atom Distance (A) Cu O B:His102 4.94 Cu CD1 B:Trp104 4.72 Cu O B:Leu160 4.58 Cu NE2 B:His161 3.92 Cu CB B:His161 3.64 Cu ND1 B:His161 1.92 Cu CD2 B:His161 4.13 Cu CE1 B:His161 2.69 Cu CG B:His161 3.11 Cu CA B:His161 4.11 Cu CB B:Cys196 3.49 Cu SG B:Cys196 2.28 Cu CA B:Cys196 4.89 Cu O B:Glu198 4.08 Cu CB B:Cys200 3.41 Cu SG B:Cys200 2.39 Cu CA B:Cys200 4.80 Cu O B:His204 4.98 Cu ND1 B:His204 4.42 Cu CA B:His204 4.79 Cu CE B:Met207 3.03 Cu CG B:Met207 3.78 Cu SD B:Met207 2.67 Cu CU B:Cu229 2.45 interactive model: Copper binding site 3 out of 6 in 1oco Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1oco. 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: His161, B: Cys196, B: Glu198, B: Ile199, B: Cys200, B: His204, B: Met207, B: Cu228, conact list: Atom Atom Distance (A) Cu ND1 B:His161 4.11 Cu CE1 B:His161 4.74 Cu O B:Cys196 4.45 Cu CB B:Cys196 3.46 Cu SG B:Cys196 2.24 Cu C B:Cys196 4.60 Cu CA B:Cys196 4.66 Cu O B:Glu198 2.38 Cu N B:Glu198 4.42 Cu C B:Glu198 3.59 Cu CA B:Glu198 4.62 Cu O B:Ile199 4.93 Cu N B:Ile199 4.33 Cu C B:Ile199 4.13 Cu CA B:Ile199 4.24 Cu N B:Cys200 3.58 Cu CB B:Cys200 3.34 Cu SG B:Cys200 2.21 Cu C B:Cys200 4.94 Cu CA B:Cys200 4.08 Cu O B:His204 3.71 Cu NE2 B:His204 4.10 Cu N B:His204 4.61 Cu CB B:His204 3.38 Cu ND1 B:His204 2.06 Cu CD2 B:His204 4.12 Cu C B:His204 3.98 Cu CE1 B:His204 3.00 Cu CG B:His204 3.02 Cu CA B:His204 3.34 Cu CG B:Met207 4.72 Cu SD B:Met207 4.39 Cu CU B:Cu228 2.45 interactive model: Copper binding site 4 out of 6 in 1oco Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1oco. 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: N: His240, N: Val243, N: His290, N: His291, N: Hea516, N: Cmo520, conact list: Atom Atom Distance (A) Cu NE2 N:His240 4.25 Cu N N:His240 4.84 Cu CB N:His240 3.49 Cu ND1 N:His240 2.15 Cu CD2 N:His240 4.30 Cu CE1 N:His240 3.10 Cu CG N:His240 3.18 Cu CA N:His240 4.05 Cu CG2 N:Val243 4.68 Cu NE2 N:His290 2.05 Cu ND1 N:His290 4.18 Cu CD2 N:His290 3.17 Cu CE1 N:His290 2.99 Cu CG N:His290 4.29 Cu NE2 N:His291 1.99 Cu ND1 N:His291 4.18 Cu CD2 N:His291 2.82 Cu CE1 N:His291 3.13 Cu CG N:His291 4.05 Cu NA N:Hea516 4.91 Cu O N:Cmo520 2.56 Cu C N:Cmo520 3.40 interactive model: Copper binding site 5 out of 6 in 1oco Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 1oco. 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: O: Trp104, O: Leu160, O: His161, O: Cys196, O: Glu198, O: Cys200, O: His204, O: Met207, O: Cu229, conact list: Atom Atom Distance (A) Cu CD1 O:Trp104 4.84 Cu O O:Leu160 4.59 Cu NE2 O:His161 4.07 Cu CB O:His161 3.70 Cu ND1 O:His161 2.04 Cu CD2 O:His161 4.25 Cu CE1 O:His161 2.83 Cu CG O:His161 3.21 Cu CA O:His161 4.11 Cu CB O:Cys196 3.35 Cu SG O:Cys196 2.23 Cu CA O:Cys196 4.72 Cu O O:Glu198 3.94 Cu N O:Cys200 4.96 Cu CB O:Cys200 3.46 Cu SG O:Cys200 2.39 Cu CA O:Cys200 4.82 Cu O O:His204 4.84 Cu ND1 O:His204 4.21 Cu CA O:His204 4.74 Cu CE O:Met207 3.02 Cu CG O:Met207 3.79 Cu SD O:Met207 2.72 Cu CU O:Cu229 2.34 interactive model: Copper binding site 6 out of 6 in 1oco Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 1oco. 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: O: Leu160, O: His161, O: Cys196, O: Glu198, O: Ile199, O: Cys200, O: His204, O: Met207, O: Cu228, conact list: Atom Atom Distance (A) Cu O O:Leu160 4.98 Cu ND1 O:His161 4.10 Cu CE1 O:His161 4.66 Cu O O:Cys196 4.55 Cu CB O:Cys196 3.64 Cu SG O:Cys196 2.37 Cu C O:Cys196 4.76 Cu CA O:Cys196 4.84 Cu O O:Glu198 2.40 Cu N O:Glu198 4.54 Cu C O:Glu198 3.60 Cu CA O:Glu198 4.68 Cu O O:Ile199 4.82 Cu N O:Ile199 4.31 Cu C O:Ile199 4.01 Cu CA O:Ile199 4.15 Cu N O:Cys200 3.43 Cu CB O:Cys200 3.23 Cu SG O:Cys200 2.09 Cu C O:Cys200 4.81 Cu CA O:Cys200 3.95 Cu O O:His204 3.73 Cu NE2 O:His204 4.13 Cu N O:His204 4.53 Cu CB O:His204 3.26 Cu ND1 O:His204 2.04 Cu CD2 O:His204 4.08 Cu C O:His204 3.96 Cu CE1 O:His204 3.06 Cu CG O:His204 2.94 Cu CA O:His204 3.27 Cu CG O:Met207 4.78 Cu SD O:Met207 4.38 Cu CU O:Cu228 2.34 interactive model: