Copper in the structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State At 100 K (pdb 3ag4)
The binding sites of Copper atom in the structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State At 100 K (pdb code 3ag4). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 3ag4 structure was solved by K.MURAMOTO, K.OHTA, K.SHINZAWA-ITOH, K.KANDA, M.TANIGUCHI, H.NABEKURA, E.YAMASHITA, T.TSUKIHARA, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 40.0-2.0 | Space group | P212121 | a (A) | 183.364 | b (A) | 206.648 | c (A) | 178.137 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 18.6 | Rfree (%) | 21.9 |
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Copper Binding Sites:Copper binding site 1 out of 6 in 3ag4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 3ag4. 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: Trp236, A: His240, A: Val243, A: His290, A: His291, A: Hea516, A: Cyn520, A: Hoh4310, | conact list:
Atom | Atom | Distance (A) | Cu | CZ3 A:Trp236 | 5.00 | Cu | O A:His240 | 4.93 | Cu | NE2 A:His240 | 4.03 | Cu | N A:His240 | 4.68 | Cu | CB A:His240 | 3.40 | Cu | ND1 A:His240 | 1.97 | Cu | CD2 A:His240 | 4.12 | Cu | C A:His240 | 4.87 | Cu | CE1 A:His240 | 2.90 | Cu | CG A:His240 | 3.03 | Cu | CA A:His240 | 3.85 | Cu | CG2 A:Val243 | 4.36 | Cu | NE2 A:His290 | 2.78 | Cu | ND1 A:His290 | 4.80 | Cu | CD2 A:His290 | 3.72 | Cu | CE1 A:His290 | 3.68 | Cu | CG A:His290 | 4.86 | Cu | NE2 A:His291 | 2.03 | Cu | ND1 A:His291 | 4.14 | Cu | CD2 A:His291 | 3.03 | Cu | CE1 A:His291 | 3.03 | Cu | CG A:His291 | 4.16 | Cu | NA A:Hea516 | 4.93 | Cu | ND A:Hea516 | 4.87 | Cu | FE A:Hea516 | 4.99 | Cu | C1A A:Hea516 | 4.93 | Cu | N A:Cyn520 | 2.26 | Cu | C A:Cyn520 | 2.88 | Cu | O A:Hoh4310 | 4.75 |
| interactive model:
| Copper binding site 2 out of 6 in 3ag4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 3ag4. 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: Cua228, | conact list:
Atom | Atom | Distance (A) | Cu | O B:His102 | 4.65 | Cu | CD1 B:Trp104 | 4.49 | Cu | CZ2 B:Trp106 | 4.99 | Cu | O B:Leu160 | 4.76 | Cu | NE2 B:His161 | 4.05 | Cu | CB B:His161 | 3.57 | Cu | ND1 B:His161 | 1.99 | Cu | CD2 B:His161 | 4.18 | Cu | CE1 B:His161 | 2.86 | Cu | CG B:His161 | 3.12 | Cu | CA B:His161 | 4.18 | Cu | CB B:Cys196 | 3.47 | Cu | SG B:Cys196 | 2.38 | Cu | CA B:Cys196 | 4.86 | Cu | O B:Glu198 | 4.05 | Cu | CB B:Cys200 | 3.33 | Cu | SG B:Cys200 | 2.37 | Cu | CA B:Cys200 | 4.78 | Cu | O B:His204 | 4.98 | Cu | ND1 B:His204 | 4.48 | Cu | CA B:His204 | 4.68 | Cu | CB B:Met207 | 4.82 | Cu | CE B:Met207 | 2.98 | Cu | CG B:Met207 | 3.49 | Cu | SD B:Met207 | 2.35 | Cu | CU1 B:Cua228 | 0.00 | Cu | CU2 B:Cua228 | 2.53 |
| interactive model:
| Copper binding site 3 out of 6 in 3ag4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 3ag4. 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: Cua228, | conact list:
Atom | Atom | Distance (A) | Cu | CB B:His161 | 4.98 | Cu | ND1 B:His161 | 4.11 | Cu | CE1 B:His161 | 4.97 | Cu | CG B:His161 | 4.97 | Cu | CA B:His161 | 4.81 | Cu | O B:Cys196 | 4.25 | Cu | CB B:Cys196 | 3.33 | Cu | SG B:Cys196 | 2.28 | Cu | C B:Cys196 | 4.18 | Cu | CA B:Cys196 | 4.39 | Cu | N B:Ser197 | 4.60 | Cu | O B:Glu198 | 2.34 | Cu | N B:Glu198 | 4.25 | Cu | C B:Glu198 | 3.56 | Cu | CA B:Glu198 | 4.60 | Cu | N B:Ile199 | 4.36 | Cu | C B:Ile199 | 4.29 | Cu | CA B:Ile199 | 4.28 | Cu | N B:Cys200 | 3.71 | Cu | CB B:Cys200 | 3.48 | Cu | SG B:Cys200 | 2.30 | Cu | CA B:Cys200 | 4.26 | Cu | O B:His204 | 3.76 | Cu | NE2 B:His204 | 4.03 | Cu | N B:His204 | 4.68 | Cu | CB B:His204 | 3.64 | Cu | ND1 B:His204 | 2.01 | Cu | CD2 B:His204 | 4.19 | Cu | C B:His204 | 4.10 | Cu | CE1 B:His204 | 2.85 | Cu | CG B:His204 | 3.16 | Cu | CA B:His204 | 3.48 | Cu | CG B:Met207 | 4.68 | Cu | SD B:Met207 | 4.38 | Cu | CU1 B:Cua228 | 2.53 | Cu | CU2 B:Cua228 | 0.00 |
| interactive model:
| Copper binding site 4 out of 6 in 3ag4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 3ag4. 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: His290, N: His291, N: Hea516, N: Cyn520, N: Hoh4406, | conact list:
Atom | Atom | Distance (A) | Cu | O N:His240 | 4.94 | Cu | NE2 N:His240 | 4.08 | Cu | N N:His240 | 4.62 | Cu | CB N:His240 | 3.29 | Cu | ND1 N:His240 | 1.98 | Cu | CD2 N:His240 | 4.13 | Cu | C N:His240 | 4.88 | Cu | CE1 N:His240 | 2.95 | Cu | CG N:His240 | 2.99 | Cu | CA N:His240 | 3.78 | Cu | CG2 N:Val243 | 4.39 | Cu | CG1 N:Val243 | 4.76 | Cu | CG2 N:Val287 | 4.89 | Cu | NE2 N:His290 | 2.64 | Cu | ND1 N:His290 | 4.67 | Cu | CD2 N:His290 | 3.67 | Cu | CE1 N:His290 | 3.50 | Cu | CG N:His290 | 4.79 | Cu | NE2 N:His291 | 1.99 | Cu | ND1 N:His291 | 4.05 | Cu | CD2 N:His291 | 3.05 | Cu | CE1 N:His291 | 2.90 | Cu | CG N:His291 | 4.14 | Cu | NA N:Hea516 | 4.93 | Cu | ND N:Hea516 | 5.00 | Cu | C1A N:Hea516 | 4.97 | Cu | N N:Cyn520 | 2.44 | Cu | C N:Cyn520 | 2.98 | Cu | O N:Hoh4406 | 4.83 |
| interactive model:
| Copper binding site 5 out of 6 in 3ag4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 3ag4. 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: His102, O: Trp104, O: Leu160, O: His161, O: Cys196, O: Glu198, O: Cys200, O: His204, O: Met207, O: Cua228, | conact list:
Atom | Atom | Distance (A) | Cu | O O:His102 | 4.68 | Cu | CD1 O:Trp104 | 4.34 | Cu | O O:Leu160 | 4.75 | Cu | NE2 O:His161 | 3.99 | Cu | CB O:His161 | 3.59 | Cu | ND1 O:His161 | 1.99 | Cu | CD2 O:His161 | 4.16 | Cu | CE1 O:His161 | 2.79 | Cu | CG O:His161 | 3.13 | Cu | CA O:His161 | 4.27 | Cu | CB O:Cys196 | 3.43 | Cu | SG O:Cys196 | 2.30 | Cu | CA O:Cys196 | 4.81 | Cu | O O:Glu198 | 4.00 | Cu | CB O:Cys200 | 3.33 | Cu | SG O:Cys200 | 2.39 | Cu | CA O:Cys200 | 4.74 | Cu | ND1 O:His204 | 4.60 | Cu | CA O:His204 | 4.78 | Cu | CB O:Met207 | 4.87 | Cu | CE O:Met207 | 3.00 | Cu | CG O:Met207 | 3.52 | Cu | SD O:Met207 | 2.40 | Cu | CU1 O:Cua228 | 0.00 | Cu | CU2 O:Cua228 | 2.63 |
| interactive model:
| Copper binding site 6 out of 6 in 3ag4
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 3ag4. 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: Cua228, | conact list:
Atom | Atom | Distance (A) | Cu | CB O:His161 | 4.99 | Cu | ND1 O:His161 | 4.11 | Cu | CE1 O:His161 | 4.95 | Cu | CA O:His161 | 4.91 | Cu | O O:Cys196 | 4.22 | Cu | CB O:Cys196 | 3.27 | Cu | SG O:Cys196 | 2.28 | Cu | C O:Cys196 | 4.24 | Cu | CA O:Cys196 | 4.39 | Cu | N O:Ser197 | 4.73 | Cu | O O:Glu198 | 2.24 | Cu | N O:Glu198 | 4.22 | Cu | C O:Glu198 | 3.43 | Cu | CA O:Glu198 | 4.43 | Cu | N O:Ile199 | 4.27 | Cu | C O:Ile199 | 4.29 | Cu | CA O:Ile199 | 4.27 | Cu | N O:Cys200 | 3.65 | Cu | CB O:Cys200 | 3.36 | Cu | SG O:Cys200 | 2.28 | Cu | CA O:Cys200 | 4.11 | Cu | O O:His204 | 3.87 | Cu | NE2 O:His204 | 4.09 | Cu | N O:His204 | 4.69 | Cu | CB O:His204 | 3.46 | Cu | ND1 O:His204 | 2.02 | Cu | CD2 O:His204 | 4.17 | Cu | C O:His204 | 4.15 | Cu | CE1 O:His204 | 2.95 | Cu | CG O:His204 | 3.07 | Cu | CA O:His204 | 3.51 | Cu | CG O:Met207 | 4.75 | Cu | SD O:Met207 | 4.44 | Cu | CU1 O:Cua228 | 2.63 | Cu | CU2 O:Cua228 | 0.00 |
| interactive model:
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