The binding sites of Copper atom in the structure of Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) From Rat (pdb code 1phm). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1phm structure was solved by S.T.PRIGGE, L.M.AMZEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 6.0-1.9 | Space group | P212121 | a (A) | 68.400 | b (A) | 68.660 | c (A) | 81.380 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 19.6 | Rfree (%) | 26.1 |
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Copper binding site 1 out of 3 in 1phm
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1phm. 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: Tyr79, A: His107, A: His108, A: His172, A: Hoh438, A: Hoh588, | conact list:
Atom | Atom | Distance (A) | Cu | OH A:Tyr79 | 4.71 | Cu | O A:His107 | 4.14 | Cu | NE2 A:His107 | 4.08 | Cu | CB A:His107 | 3.26 | Cu | ND1 A:His107 | 1.92 | Cu | CD2 A:His107 | 4.09 | Cu | C A:His107 | 3.70 | Cu | CE1 A:His107 | 2.94 | Cu | CG A:His107 | 2.93 | Cu | CA A:His107 | 4.11 | Cu | O A:His108 | 4.93 | Cu | NE2 A:His108 | 4.08 | Cu | N A:His108 | 3.50 | Cu | CB A:His108 | 3.26 | Cu | ND1 A:His108 | 1.92 | Cu | CD2 A:His108 | 4.08 | Cu | C A:His108 | 4.86 | Cu | CE1 A:His108 | 2.94 | Cu | CG A:His108 | 2.93 | Cu | CA A:His108 | 3.98 | Cu | NE2 A:His172 | 4.37 | Cu | CB A:His172 | 3.75 | Cu | ND1 A:His172 | 2.29 | Cu | CD2 A:His172 | 4.47 | Cu | CE1 A:His172 | 3.17 | Cu | CG A:His172 | 3.37 | Cu | O A:Hoh438 | 4.02 | Cu | O A:Hoh588 | 4.88 |
| interactive model:
| Copper binding site 2 out of 3 in 1phm
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1phm. 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: His242, A: His244, A: Gly307, A: Met314, A: Hoh360, A: Hoh594, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His242 | 1.91 | Cu | ND1 A:His242 | 4.06 | Cu | CD2 A:His242 | 2.94 | Cu | CE1 A:His242 | 2.92 | Cu | CG A:His242 | 4.09 | Cu | NE2 A:His244 | 2.09 | Cu | ND1 A:His244 | 4.24 | Cu | CD2 A:His244 | 3.03 | Cu | CE1 A:His244 | 3.14 | Cu | CG A:His244 | 4.22 | Cu | O A:Gly307 | 4.87 | Cu | CB A:Met314 | 3.69 | Cu | CE A:Met314 | 3.62 | Cu | CG A:Met314 | 3.34 | Cu | SD A:Met314 | 2.42 | Cu | O A:Hoh360 | 2.28 | Cu | O A:Hoh594 | 4.48 |
| interactive model:
| Copper binding site 3 out of 3 in 1phm
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1phm. 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: His235, A: Asp282, A: Azi361, A: Gol362, A: Hoh363, A: Hoh370, A: Hoh424, A: Hoh525, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His235 | 2.08 | Cu | ND1 A:His235 | 4.22 | Cu | CD2 A:His235 | 2.93 | Cu | CE1 A:His235 | 3.17 | Cu | CG A:His235 | 4.14 | Cu | CB A:Asp282 | 4.08 | Cu | OD1 A:Asp282 | 4.45 | Cu | CG A:Asp282 | 4.53 | Cu | N1 A:Azi361 | 1.84 | Cu | N3 A:Azi361 | 3.95 | Cu | N2 A:Azi361 | 2.81 | Cu | O2 A:Gol362 | 2.28 | Cu | C1 A:Gol362 | 2.80 | Cu | O1 A:Gol362 | 2.26 | Cu | C3 A:Gol362 | 4.33 | Cu | C2 A:Gol362 | 2.90 | Cu | O A:Hoh363 | 2.01 | Cu | O A:Hoh370 | 4.53 | Cu | O A:Hoh424 | 4.47 | Cu | O A:Hoh525 | 4.62 |
| interactive model:
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