Copper in the structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb 1ocr)

The binding sites of Copper atom in the structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 1ocr). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1ocr structure was solved by T.TSUKIHARA, M.YAO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-2.4 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 (%) 20.3 Rfree (%) 24.7 Copper Binding Sites: Copper binding site 1 out of 6 in 1ocr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1ocr. 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: His290, A: His291, A: Hea516, conact list: Atom Atom Distance (A) Cu NE2 A:His240 4.29 Cu N A:His240 4.76 Cu CB A:His240 3.40 Cu ND1 A:His240 2.16 Cu CD2 A:His240 4.29 Cu CE1 A:His240 3.17 Cu CG A:His240 3.13 Cu CA A:His240 3.93 Cu CG2 A:Val243 4.82 Cu NE2 A:His290 1.96 Cu ND1 A:His290 4.11 Cu CD2 A:His290 3.04 Cu CE1 A:His290 2.95 Cu CG A:His290 4.18 Cu NE2 A:His291 1.91 Cu ND1 A:His291 4.07 Cu CD2 A:His291 2.85 Cu CE1 A:His291 2.98 Cu CG A:His291 4.03 Cu NA A:Hea516 4.75 Cu C2A A:Hea516 4.98 Cu C4A A:Hea516 4.89 Cu C1A A:Hea516 4.72 interactive model: Copper binding site 2 out of 6 in 1ocr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1ocr. 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: Trp106, 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 4.92 Cu CD1 B:Trp104 4.80 Cu CZ2 B:Trp106 4.95 Cu O B:Leu160 4.64 Cu NE2 B:His161 3.91 Cu CB B:His161 3.81 Cu ND1 B:His161 1.96 Cu CD2 B:His161 4.18 Cu CE1 B:His161 2.63 Cu CG B:His161 3.20 Cu CA B:His161 4.25 Cu CB B:Cys196 3.43 Cu SG B:Cys196 2.21 Cu CA B:Cys196 4.80 Cu O B:Glu198 4.07 Cu N B:Cys200 4.94 Cu CB B:Cys200 3.29 Cu SG B:Cys200 2.34 Cu CA B:Cys200 4.70 Cu O B:His204 4.99 Cu ND1 B:His204 4.52 Cu CA B:His204 4.84 Cu CB B:Met207 4.99 Cu CE B:Met207 2.96 Cu CG B:Met207 3.69 Cu SD B:Met207 2.67 Cu CU B:Cu229 2.58 interactive model: Copper binding site 3 out of 6 in 1ocr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1ocr. 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: Ser197, B: Glu198, B: Ile199, B: Cys200, B: His204, B: Met207, B: Cu228, conact list: Atom Atom Distance (A) Cu ND1 B:His161 4.19 Cu CE1 B:His161 4.84 Cu O B:Cys196 4.35 Cu CB B:Cys196 3.19 Cu SG B:Cys196 2.27 Cu C B:Cys196 4.34 Cu CA B:Cys196 4.37 Cu N B:Ser197 4.82 Cu O B:Glu198 2.41 Cu N B:Glu198 4.21 Cu C B:Glu198 3.56 Cu CA B:Glu198 4.55 Cu N B:Ile199 4.30 Cu C B:Ile199 4.16 Cu CA B:Ile199 4.22 Cu N B:Cys200 3.63 Cu CB B:Cys200 3.45 Cu SG B:Cys200 2.21 Cu CA B:Cys200 4.18 Cu O B:His204 3.55 Cu NE2 B:His204 4.10 Cu N B:His204 4.80 Cu CB B:His204 3.37 Cu ND1 B:His204 1.97 Cu CD2 B:His204 4.13 Cu C B:His204 3.99 Cu CE1 B:His204 2.95 Cu CG B:His204 3.00 Cu CA B:His204 3.50 Cu CG B:Met207 4.69 Cu SD B:Met207 4.47 Cu CU B:Cu228 2.58 interactive model: Copper binding site 4 out of 6 in 1ocr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1ocr. 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: Val287, N: Trp288, N: His290, N: His291, N: Hea516, conact list: Atom Atom Distance (A) Cu NE2 N:His240 4.27 Cu N N:His240 4.69 Cu CB N:His240 3.36 Cu ND1 N:His240 2.13 Cu CD2 N:His240 4.25 Cu CE1 N:His240 3.15 Cu CG N:His240 3.10 Cu CA N:His240 3.88 Cu CG2 N:Val243 4.78 Cu CG2 N:Val287 4.96 Cu O N:Trp288 4.98 Cu NE2 N:His290 1.99 Cu ND1 N:His290 4.11 Cu CD2 N:His290 3.08 Cu CE1 N:His290 2.94 Cu CG N:His290 4.20 Cu NE2 N:His291 1.96 Cu ND1 N:His291 4.13 Cu CD2 N:His291 2.90 Cu CE1 N:His291 3.03 Cu CG N:His291 4.09 Cu NA N:Hea516 4.80 Cu C4A N:Hea516 4.93 Cu C1A N:Hea516 4.80 interactive model: Copper binding site 5 out of 6 in 1ocr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 1ocr. 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: Trp106, 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 4.88 Cu CZ2 O:Trp106 4.99 Cu O O:Leu160 4.62 Cu NE2 O:His161 3.98 Cu CB O:His161 3.80 Cu ND1 O:His161 1.99 Cu CD2 O:His161 4.23 Cu CE1 O:His161 2.71 Cu CG O:His161 3.22 Cu CA O:His161 4.19 Cu CB O:Cys196 3.41 Cu SG O:Cys196 2.20 Cu CA O:Cys196 4.75 Cu O O:Glu198 3.90 Cu N O:Cys200 4.76 Cu CB O:Cys200 3.21 Cu SG O:Cys200 2.25 Cu CA O:Cys200 4.58 Cu O O:His204 4.93 Cu ND1 O:His204 4.34 Cu CA O:His204 4.81 Cu CE O:Met207 3.07 Cu CG O:Met207 3.75 Cu SD O:Met207 2.73 Cu CU O:Cu229 2.32 interactive model: Copper binding site 6 out of 6 in 1ocr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 1ocr. 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: His161, O: Cys196, O: Ser197, O: Glu198, O: Ile199, O: Cys200, O: His204, O: Met207, O: Cu228, conact list: Atom Atom Distance (A) Cu ND1 O:His161 4.06 Cu CE1 O:His161 4.71 Cu O O:Cys196 4.38 Cu CB O:Cys196 3.20 Cu SG O:Cys196 2.29 Cu C O:Cys196 4.40 Cu CA O:Cys196 4.41 Cu N O:Ser197 4.88 Cu O O:Glu198 2.44 Cu N O:Glu198 4.26 Cu C O:Glu198 3.59 Cu CA O:Glu198 4.59 Cu N O:Ile199 4.35 Cu C O:Ile199 4.19 Cu CA O:Ile199 4.27 Cu N O:Cys200 3.57 Cu CB O:Cys200 3.39 Cu SG O:Cys200 2.21 Cu CA O:Cys200 4.11 Cu O O:His204 3.63 Cu NE2 O:His204 4.19 Cu N O:His204 4.83 Cu CB O:His204 3.42 Cu ND1 O:His204 2.04 Cu CD2 O:His204 4.22 Cu C O:His204 4.05 Cu CE1 O:His204 3.02 Cu CG O:His204 3.08 Cu CA O:His204 3.55 Cu CG O:Met207 4.62 Cu SD O:Met207 4.34 Cu CU O:Cu228 2.32 interactive model: