Copper in the structure of The 1.37-A Crystal Structure Of The Hydroxylamine-Induced Deoxy-Form of the Copper-Bound Tyrosinase in Complex With A Caddie Protein From Streptomyces Castaneoglobisporus (pdb 2zmz)
The binding sites of Copper atom in the structure of The 1.37-A Crystal Structure Of The Hydroxylamine-Induced Deoxy-Form of the Copper-Bound Tyrosinase in Complex With A Caddie Protein From Streptomyces Castaneoglobisporus (pdb code 2zmz). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2zmz structure was solved by Y.MATOBA, M.SUGIYAMA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 30.0-1.4 | Space group | P21212 | a (A) | 65.180 | b (A) | 98.030 | c (A) | 55.200 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 18.6 | Rfree (%) | 23.2 |
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Copper Binding Sites:Copper binding site 1 out of 4 in 2zmz
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2zmz. 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: His38, A: Gly53, A: His54, A: Trp62, A: His63, A: Phe212, A: His216, B: Tyr98, A: Cu1302, B: Hoh340, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His38 | 1.86 | Cu | ND1 A:His38 | 3.93 | Cu | CD2 A:His38 | 2.77 | Cu | CE1 A:His38 | 2.88 | Cu | CG A:His38 | 3.92 | Cu | O A:Gly53 | 5.00 | Cu | NE2 A:His54 | 2.12 | Cu | ND1 A:His54 | 4.26 | Cu | CD2 A:His54 | 3.00 | Cu | CE1 A:His54 | 3.19 | Cu | CG A:His54 | 4.18 | Cu | CZ3 A:Trp62 | 4.71 | Cu | NE2 A:His63 | 2.16 | Cu | ND1 A:His63 | 4.14 | Cu | CD2 A:His63 | 3.35 | Cu | CE1 A:His63 | 2.92 | Cu | CG A:His63 | 4.38 | Cu | CE2 A:Phe212 | 4.30 | Cu | CZ A:Phe212 | 4.10 | Cu | NE2 A:His216 | 4.25 | Cu | CE1 A:His216 | 4.54 | Cu | OH B:Tyr98 | 4.35 | Cu | CU A:Cu1302 | 4.07 | Cu | O B:Hoh340 | 2.35 |
| interactive model:
| Copper binding site 2 out of 4 in 2zmz
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2zmz. 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: Phe59, A: His63, A: His190, A: His194, A: Phe212, A: His215, A: His216, B: Tyr98, A: Cu1301, B: Hoh340, | conact list:
Atom | Atom | Distance (A) | Cu | CE1 A:Phe59 | 4.90 | Cu | NE2 A:His63 | 4.66 | Cu | NE2 A:His190 | 2.01 | Cu | ND1 A:His190 | 4.10 | Cu | CD2 A:His190 | 2.99 | Cu | CE1 A:His190 | 3.00 | Cu | CG A:His190 | 4.13 | Cu | NE2 A:His194 | 1.98 | Cu | ND1 A:His194 | 4.10 | Cu | CD2 A:His194 | 3.05 | Cu | CE1 A:His194 | 2.96 | Cu | CG A:His194 | 4.18 | Cu | CE2 A:Phe212 | 4.06 | Cu | CD2 A:Phe212 | 4.75 | Cu | CZ A:Phe212 | 4.67 | Cu | NE2 A:His215 | 4.52 | Cu | CD2 A:His215 | 4.31 | Cu | NE2 A:His216 | 2.01 | Cu | ND1 A:His216 | 4.06 | Cu | CD2 A:His216 | 3.10 | Cu | CE1 A:His216 | 2.90 | Cu | CG A:His216 | 4.18 | Cu | CE2 B:Tyr98 | 4.13 | Cu | CZ B:Tyr98 | 4.36 | Cu | OH B:Tyr98 | 4.08 | Cu | CU A:Cu1301 | 4.07 | Cu | O B:Hoh340 | 2.03 |
| interactive model:
| Copper binding site 3 out of 4 in 2zmz
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2zmz. 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: Ile42, A: Met43, B: His82, B: Val83, B: Met84, B: Ile92, B: His97, B: No3304, A: Hoh412, | conact list:
Atom | Atom | Distance (A) | Cu | O A:Ile42 | 3.30 | Cu | C A:Ile42 | 4.28 | Cu | O A:Met43 | 4.01 | Cu | N A:Met43 | 4.54 | Cu | CB A:Met43 | 4.83 | Cu | C A:Met43 | 4.25 | Cu | CG A:Met43 | 4.87 | Cu | CA A:Met43 | 3.85 | Cu | NE2 B:His82 | 2.04 | Cu | NE2 B:His82 | 4.87 | Cu | ND1 B:His82 | 4.10 | Cu | ND1 B:His82 | 3.56 | Cu | CD2 B:His82 | 3.10 | Cu | CE1 B:His82 | 2.98 | Cu | CE1 B:His82 | 3.56 | Cu | CG B:His82 | 4.23 | Cu | CG B:His82 | 4.92 | Cu | C B:Val83 | 4.95 | Cu | N B:Met84 | 4.75 | Cu | CB B:Met84 | 3.46 | Cu | CE B:Met84 | 3.26 | Cu | CG B:Met84 | 3.26 | Cu | SD B:Met84 | 2.36 | Cu | CA B:Met84 | 4.68 | Cu | CD1 B:Ile92 | 4.78 | Cu | CG1 B:Ile92 | 4.84 | Cu | NE2 B:His97 | 2.30 | Cu | NE2 B:His97 | 2.97 | Cu | ND1 B:His97 | 4.15 | Cu | ND1 B:His97 | 3.94 | Cu | CD2 B:His97 | 3.52 | Cu | CD2 B:His97 | 4.20 | Cu | CE1 B:His97 | 2.90 | Cu | CE1 B:His97 | 2.78 | Cu | CG B:His97 | 4.47 | Cu | CG B:His97 | 4.69 | Cu | O1 B:No3304 | 3.03 | Cu | O2 B:No3304 | 2.98 | Cu | N B:No3304 | 2.58 | Cu | O3 B:No3304 | 2.52 | Cu | O A:Hoh412 | 4.55 |
| interactive model:
| Copper binding site 4 out of 4 in 2zmz
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2zmz. 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: Met43, B: Glu67, B: His68, B: Gly69, B: His82, B: Hoh424, | conact list:
Atom | Atom | Distance (A) | Cu | O A:Met43 | 4.16 | Cu | O B:Glu67 | 4.80 | Cu | N B:Glu67 | 4.49 | Cu | OE1 B:Glu67 | 2.30 | Cu | CB B:Glu67 | 2.16 | Cu | OE2 B:Glu67 | 4.13 | Cu | CD B:Glu67 | 2.89 | Cu | C B:Glu67 | 3.59 | Cu | CG B:Glu67 | 2.80 | Cu | CA B:Glu67 | 3.44 | Cu | O B:His68 | 4.14 | Cu | NE2 B:His68 | 3.41 | Cu | N B:His68 | 2.79 | Cu | CB B:His68 | 3.85 | Cu | ND1 B:His68 | 1.69 | Cu | CD2 B:His68 | 3.82 | Cu | C B:His68 | 4.07 | Cu | CE1 B:His68 | 2.15 | Cu | CG B:His68 | 3.01 | Cu | CA B:His68 | 3.70 | Cu | O B:Gly69 | 4.84 | Cu | N B:Gly69 | 4.86 | Cu | C B:Gly69 | 4.99 | Cu | NE2 B:His82 | 4.92 | Cu | NE2 B:His82 | 1.96 | Cu | ND1 B:His82 | 3.44 | Cu | ND1 B:His82 | 4.08 | Cu | CD2 B:His82 | 2.88 | Cu | CE1 B:His82 | 3.59 | Cu | CE1 B:His82 | 3.02 | Cu | CG B:His82 | 4.76 | Cu | CG B:His82 | 4.06 | Cu | O B:Hoh424 | 4.71 |
| interactive model:
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