Copper in the structure of Crystal Structure of The Copper-Bound Tyrosinase In Complex With A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours (pdb 2zwg)
The binding sites of Copper atom in the structure of Crystal Structure of The Copper-Bound Tyrosinase In Complex With A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours (pdb code 2zwg). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2zwg structure was solved by Y.MATOBA, M.SUGIYAMA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 30.0-1.3 | Space group | P21212 | a (A) | 65.240 | b (A) | 97.760 | c (A) | 55.070 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 17.9 | Rfree (%) | 22.5 |
|
Copper Binding Sites:Copper binding site 1 out of 6 in 2zwg
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2zwg. 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: Ile42, A: His54, A: Phe59, A: His63, A: His190, A: His194, A: Phe212, A: His216, B: Dah98, A: Cu501, A: Cu502, A: Hoh530, B: Hoh546, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His38 | 2.02 | Cu | NE2 A:His38 | 2.57 | Cu | ND1 A:His38 | 4.10 | Cu | ND1 A:His38 | 4.68 | Cu | CD2 A:His38 | 3.05 | Cu | CD2 A:His38 | 3.04 | Cu | CE1 A:His38 | 2.96 | Cu | CE1 A:His38 | 3.82 | Cu | CG A:His38 | 4.17 | Cu | CG A:His38 | 4.36 | Cu | CD1 A:Ile42 | 4.73 | Cu | NE2 A:His54 | 2.05 | Cu | ND1 A:His54 | 4.19 | Cu | CD2 A:His54 | 3.00 | Cu | CE1 A:His54 | 3.08 | Cu | CG A:His54 | 4.14 | Cu | CE1 A:Phe59 | 4.81 | Cu | NE2 A:His63 | 2.52 | Cu | ND1 A:His63 | 4.36 | Cu | CD2 A:His63 | 3.70 | Cu | CE1 A:His63 | 3.14 | Cu | CG A:His63 | 4.68 | Cu | NE2 A:His190 | 4.59 | Cu | CE1 A:His190 | 4.94 | Cu | NE2 A:His194 | 4.79 | Cu | CE2 A:Phe212 | 4.37 | Cu | CZ A:Phe212 | 4.40 | Cu | NE2 A:His216 | 4.02 | Cu | CD2 A:His216 | 4.99 | Cu | CE1 A:His216 | 4.41 | Cu | CE2 B:Dah98 | 4.37 | Cu | OE2 B:Dah98 | 3.20 | Cu | CZ B:Dah98 | 4.58 | Cu | OZ B:Dah98 | 3.72 | Cu | CU A:Cu501 | 0.00 | Cu | CU A:Cu501 | 1.78 | Cu | CU A:Cu502 | 3.24 | Cu | O A:Hoh530 | 1.93 | Cu | O B:Hoh546 | 1.93 |
| interactive model:
| Copper binding site 2 out of 6 in 2zwg
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2zwg. 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: Ile42, A: His54, A: His63, A: His190, A: His194, A: Ser206, A: Phe212, A: His216, B: Dah98, A: Cu501, A: Cu502, A: Hoh530, B: Hoh546, B: Hoh558, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His38 | 2.24 | Cu | NE2 A:His38 | 2.09 | Cu | ND1 A:His38 | 3.62 | Cu | ND1 A:His38 | 4.06 | Cu | CD2 A:His38 | 3.61 | Cu | CD2 A:His38 | 3.25 | Cu | CE1 A:His38 | 2.29 | Cu | CE1 A:His38 | 2.86 | Cu | CG A:His38 | 4.27 | Cu | CG A:His38 | 4.29 | Cu | CB A:Ile42 | 4.64 | Cu | CD1 A:Ile42 | 3.26 | Cu | CG1 A:Ile42 | 4.13 | Cu | NE2 A:His54 | 2.60 | Cu | ND1 A:His54 | 4.58 | Cu | CD2 A:His54 | 3.32 | Cu | CE1 A:His54 | 3.59 | Cu | CG A:His54 | 4.44 | Cu | NE2 A:His63 | 4.30 | Cu | CE1 A:His63 | 4.84 | Cu | NE2 A:His190 | 4.91 | Cu | NE2 A:His194 | 4.39 | Cu | CE1 A:His194 | 4.51 | Cu | OG A:Ser206 | 4.16 | Cu | CE2 A:Phe212 | 4.66 | Cu | NE2 A:His216 | 4.99 | Cu | CE2 B:Dah98 | 3.05 | Cu | CD2 B:Dah98 | 4.39 | Cu | OE2 B:Dah98 | 2.18 | Cu | CZ B:Dah98 | 3.00 | Cu | CE1 B:Dah98 | 4.32 | Cu | OZ B:Dah98 | 2.12 | Cu | CU A:Cu501 | 1.78 | Cu | CU A:Cu501 | 0.00 | Cu | CU A:Cu502 | 3.52 | Cu | O A:Hoh530 | 2.08 | Cu | O B:Hoh546 | 2.73 | Cu | O B:Hoh558 | 4.60 |
| interactive model:
| Copper binding site 3 out of 6 in 2zwg
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2zwg. 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: His54, A: Phe59, A: His63, A: His190, A: His194, A: Phe212, A: His215, A: His216, B: Dah98, A: Cu501, A: Hoh530, B: Hoh546, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His38 | 4.71 | Cu | NE2 A:His54 | 4.87 | Cu | CZ A:Phe59 | 4.98 | Cu | CE1 A:Phe59 | 4.64 | Cu | NE2 A:His63 | 4.35 | Cu | CD2 A:His63 | 4.83 | Cu | NE2 A:His190 | 1.93 | Cu | ND1 A:His190 | 4.04 | Cu | CD2 A:His190 | 3.02 | Cu | CE1 A:His190 | 2.86 | Cu | CG A:His190 | 4.13 | Cu | NE2 A:His194 | 2.07 | Cu | ND1 A:His194 | 4.16 | Cu | CD2 A:His194 | 3.10 | Cu | CE1 A:His194 | 3.03 | Cu | CG A:His194 | 4.21 | Cu | CE2 A:Phe212 | 4.32 | Cu | CZ A:Phe212 | 4.86 | Cu | NE2 A:His215 | 4.80 | Cu | CD2 A:His215 | 4.64 | Cu | NE2 A:His216 | 2.15 | Cu | ND1 A:His216 | 4.18 | Cu | CD2 A:His216 | 3.29 | Cu | CE1 A:His216 | 2.97 | Cu | CG A:His216 | 4.34 | Cu | CE2 B:Dah98 | 3.74 | Cu | CD2 B:Dah98 | 4.57 | Cu | OE2 B:Dah98 | 3.05 | Cu | CZ B:Dah98 | 4.17 | Cu | OZ B:Dah98 | 3.96 | Cu | CU A:Cu501 | 3.24 | Cu | CU A:Cu501 | 3.52 | Cu | O A:Hoh530 | 1.97 | Cu | O B:Hoh546 | 2.28 |
| interactive model:
| Copper binding site 4 out of 6 in 2zwg
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2zwg. 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: Pro231, A: His277, A: Hoh829, A: Hoh839, A: Hoh924, | conact list:
Atom | Atom | Distance (A) | Cu | CG A:Pro231 | 4.68 | Cu | NE2 A:His277 | 2.01 | Cu | ND1 A:His277 | 3.99 | Cu | CD2 A:His277 | 3.18 | Cu | CE1 A:His277 | 2.78 | Cu | CG A:His277 | 4.21 | Cu | O A:Hoh829 | 2.53 | Cu | O A:Hoh839 | 4.72 | Cu | O A:Hoh924 | 2.63 |
| interactive model:
| Copper binding site 5 out of 6 in 2zwg
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 2zwg. 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, A: Hoh540, | conact list:
Atom | Atom | Distance (A) | Cu | O A:Ile42 | 3.24 | Cu | C A:Ile42 | 4.18 | Cu | O A:Met43 | 4.02 | Cu | N A:Met43 | 4.41 | Cu | CB A:Met43 | 4.64 | Cu | C A:Met43 | 4.18 | Cu | CG A:Met43 | 4.76 | Cu | CA A:Met43 | 3.72 | Cu | NE2 B:His82 | 2.00 | Cu | NE2 B:His82 | 3.33 | Cu | ND1 B:His82 | 4.01 | Cu | ND1 B:His82 | 3.11 | Cu | CD2 B:His82 | 3.11 | Cu | CD2 B:His82 | 4.44 | Cu | CE1 B:His82 | 2.86 | Cu | CE1 B:His82 | 2.27 | Cu | CG B:His82 | 4.17 | Cu | CG B:His82 | 4.35 | Cu | C B:Val83 | 4.98 | Cu | N B:Met84 | 4.80 | Cu | CB B:Met84 | 3.60 | Cu | CE B:Met84 | 3.39 | Cu | CG B:Met84 | 2.91 | Cu | SD B:Met84 | 2.20 | Cu | CA B:Met84 | 4.76 | Cu | CG1 B:Ile92 | 4.86 | Cu | NE2 B:His97 | 2.15 | Cu | ND1 B:His97 | 4.09 | Cu | CD2 B:His97 | 3.30 | Cu | CE1 B:His97 | 2.89 | Cu | CG B:His97 | 4.31 | Cu | O A:Hoh540 | 4.62 |
| interactive model:
| Copper binding site 6 out of 6 in 2zwg
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 2zwg. 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: His82, B: Hoh598, | conact list:
Atom | Atom | Distance (A) | Cu | O A:Met43 | 4.02 | Cu | NE2 B:His82 | 3.17 | Cu | ND1 B:His82 | 3.72 | Cu | CD2 B:His82 | 3.22 | Cu | CE1 B:His82 | 3.78 | Cu | CE1 B:His82 | 4.48 | Cu | CG B:His82 | 4.56 | Cu | O B:Hoh598 | 4.76 |
| interactive model:
|
|
|
|
|