Copper in the structure of A High-Dose Crystal Structure of A Recombinant Melanocarbus Albomyces Laccase (pdb 2ih9)
The binding sites of Copper atom in the structure of A High-Dose Crystal Structure of A Recombinant Melanocarbus Albomyces Laccase (pdb code 2ih9). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2ih9 structure was solved by N.HAKULINEN, J.ROUVINEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 25.0-2.0 | Space group | C121 | a (A) | 174.490 | b (A) | 62.330 | c (A) | 125.100 | alpha (°) | 90.00 | beta (°) | 96.25 | gamma (°) | 90.00 | Rfactor (%) | 26.3 | Rfree (%) | 29.9 |
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Copper Binding Sites:Copper binding site 1 out of 8 in 2ih9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2ih9. 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: Pro430, A: His431, A: Pro432, A: Cys503, A: Ile505, A: His508, A: Leu513, | conact list:
Atom | Atom | Distance (A) | Cu | O A:Pro430 | 4.33 | Cu | NE2 A:His431 | 3.97 | Cu | N A:His431 | 4.87 | Cu | CB A:His431 | 3.46 | Cu | ND1 A:His431 | 1.94 | Cu | CD2 A:His431 | 4.07 | Cu | C A:His431 | 4.90 | Cu | CE1 A:His431 | 2.84 | Cu | CG A:His431 | 3.01 | Cu | CA A:His431 | 3.91 | Cu | N A:Pro432 | 4.95 | Cu | CD A:Pro432 | 4.48 | Cu | CB A:Cys503 | 3.36 | Cu | SG A:Cys503 | 2.16 | Cu | CA A:Cys503 | 4.71 | Cu | N A:Ile505 | 4.96 | Cu | CB A:Ile505 | 4.07 | Cu | CD1 A:Ile505 | 3.82 | Cu | CG2 A:Ile505 | 4.93 | Cu | CG1 A:Ile505 | 4.24 | Cu | NE2 A:His508 | 4.00 | Cu | CB A:His508 | 3.27 | Cu | ND1 A:His508 | 1.91 | Cu | CD2 A:His508 | 4.03 | Cu | CE1 A:His508 | 2.90 | Cu | CG A:His508 | 2.91 | Cu | CA A:His508 | 4.79 | Cu | CD1 A:Leu513 | 3.85 |
| interactive model:
| Copper binding site 2 out of 8 in 2ih9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2ih9. 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: His93, A: His138, A: His140, A: His434, A: His436, A: Leu500, A: His502, A: Cu603, A: Cu604, A: Hoh1160, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His93 | 4.23 | Cu | CD2 A:His93 | 4.05 | Cu | CG A:His93 | 4.81 | Cu | CE1 A:His138 | 4.81 | Cu | NE2 A:His140 | 1.98 | Cu | ND1 A:His140 | 4.00 | Cu | CD2 A:His140 | 3.11 | Cu | CE1 A:His140 | 2.82 | Cu | CG A:His140 | 4.17 | Cu | NE2 A:His434 | 4.59 | Cu | CD2 A:His434 | 4.09 | Cu | NE2 A:His436 | 1.91 | Cu | ND1 A:His436 | 3.85 | Cu | CD2 A:His436 | 3.11 | Cu | CE1 A:His436 | 2.64 | Cu | CG A:His436 | 4.10 | Cu | CB A:Leu500 | 4.76 | Cu | CD1 A:Leu500 | 4.55 | Cu | NE2 A:His502 | 1.92 | Cu | ND1 A:His502 | 3.92 | Cu | CD2 A:His502 | 3.00 | Cu | CE1 A:His502 | 2.78 | Cu | CG A:His502 | 4.05 | Cu | CU A:Cu603 | 4.86 | Cu | CU A:Cu604 | 4.07 | Cu | O A:Hoh1160 | 2.60 |
| interactive model:
| Copper binding site 3 out of 8 in 2ih9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2ih9. 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: His93, A: His95, A: Trp136, A: His138, A: His434, A: His504, A: Cu602, A: Cu604, A: Hoh1160, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His93 | 4.47 | Cu | CD2 A:His93 | 3.97 | Cu | NE2 A:His95 | 4.00 | Cu | CB A:His95 | 3.44 | Cu | ND1 A:His95 | 1.95 | Cu | CD2 A:His95 | 4.09 | Cu | CE1 A:His95 | 2.85 | Cu | CG A:His95 | 3.02 | Cu | CA A:His95 | 4.68 | Cu | CZ2 A:Trp136 | 3.72 | Cu | CE2 A:Trp136 | 4.14 | Cu | NE1 A:Trp136 | 4.42 | Cu | CH2 A:Trp136 | 4.29 | Cu | NE2 A:His138 | 1.94 | Cu | ND1 A:His138 | 4.00 | Cu | CD2 A:His138 | 2.92 | Cu | CE1 A:His138 | 2.92 | Cu | CG A:His138 | 4.04 | Cu | NE2 A:His434 | 4.38 | Cu | CD2 A:His434 | 4.31 | Cu | NE2 A:His504 | 1.99 | Cu | ND1 A:His504 | 4.02 | Cu | CD2 A:His504 | 3.09 | Cu | CE1 A:His504 | 2.86 | Cu | CG A:His504 | 4.17 | Cu | CU A:Cu602 | 4.86 | Cu | CU A:Cu604 | 3.94 | Cu | O A:Hoh1160 | 2.32 |
| interactive model:
| Copper binding site 4 out of 8 in 2ih9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2ih9. 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: His93, A: His95, A: Gly96, A: His138, A: His434, A: Leu435, A: His436, A: Cu602, A: Cu603, A: Cl610, A: Hoh1160, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 A:His93 | 1.89 | Cu | ND1 A:His93 | 4.00 | Cu | CD2 A:His93 | 2.83 | Cu | CE1 A:His93 | 2.93 | Cu | CG A:His93 | 3.99 | Cu | NE2 A:His95 | 4.56 | Cu | N A:His95 | 4.62 | Cu | CB A:His95 | 3.93 | Cu | ND1 A:His95 | 3.76 | Cu | CD2 A:His95 | 4.21 | Cu | C A:His95 | 4.79 | Cu | CE1 A:His95 | 4.31 | Cu | CG A:His95 | 3.68 | Cu | CA A:His95 | 3.80 | Cu | N A:Gly96 | 4.66 | Cu | NE2 A:His138 | 4.96 | Cu | NE2 A:His434 | 1.91 | Cu | ND1 A:His434 | 4.00 | Cu | CD2 A:His434 | 2.85 | Cu | CE1 A:His434 | 2.93 | Cu | CG A:His434 | 4.00 | Cu | O A:Leu435 | 4.89 | Cu | NE2 A:His436 | 3.20 | Cu | N A:His436 | 4.94 | Cu | CB A:His436 | 4.65 | Cu | ND1 A:His436 | 4.10 | Cu | CD2 A:His436 | 3.12 | Cu | CE1 A:His436 | 3.82 | Cu | CG A:His436 | 3.73 | Cu | CA A:His436 | 4.54 | Cu | CU A:Cu602 | 4.07 | Cu | CU A:Cu603 | 3.94 | Cu | CL A:Cl610 | 2.93 | Cu | O A:Hoh1160 | 3.52 |
| interactive model:
| Copper binding site 5 out of 8 in 2ih9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 2ih9. 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: Pro430, B: His431, B: Pro432, B: Cys503, B: Ile505, B: His508, B: Leu513, | conact list:
Atom | Atom | Distance (A) | Cu | O B:Pro430 | 4.49 | Cu | NE2 B:His431 | 3.96 | Cu | N B:His431 | 4.90 | Cu | CB B:His431 | 3.37 | Cu | ND1 B:His431 | 1.92 | Cu | CD2 B:His431 | 4.03 | Cu | C B:His431 | 4.87 | Cu | CE1 B:His431 | 2.85 | Cu | CG B:His431 | 2.95 | Cu | CA B:His431 | 3.91 | Cu | N B:Pro432 | 4.90 | Cu | CD B:Pro432 | 4.42 | Cu | CB B:Cys503 | 3.33 | Cu | SG B:Cys503 | 2.16 | Cu | CA B:Cys503 | 4.70 | Cu | N B:Ile505 | 4.99 | Cu | CB B:Ile505 | 4.16 | Cu | CD1 B:Ile505 | 4.02 | Cu | CG2 B:Ile505 | 4.99 | Cu | CG1 B:Ile505 | 4.40 | Cu | NE2 B:His508 | 4.01 | Cu | CB B:His508 | 3.27 | Cu | ND1 B:His508 | 1.95 | Cu | CD2 B:His508 | 4.03 | Cu | CE1 B:His508 | 2.93 | Cu | CG B:His508 | 2.92 | Cu | CA B:His508 | 4.80 | Cu | CD1 B:Leu513 | 3.83 |
| interactive model:
| Copper binding site 6 out of 8 in 2ih9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 2ih9. 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: His93, B: His138, B: His140, B: His434, B: His436, B: Leu500, B: His502, B: Cu603, B: Cu604, B: Hoh1087, B: Hoh1141, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 B:His93 | 4.04 | Cu | CD2 B:His93 | 3.95 | Cu | CE1 B:His93 | 4.84 | Cu | CG B:His93 | 4.74 | Cu | CE1 B:His138 | 4.86 | Cu | NE2 B:His140 | 2.00 | Cu | ND1 B:His140 | 4.05 | Cu | CD2 B:His140 | 3.07 | Cu | CE1 B:His140 | 2.90 | Cu | CG B:His140 | 4.16 | Cu | NE2 B:His434 | 4.54 | Cu | CD2 B:His434 | 4.09 | Cu | NE2 B:His436 | 1.88 | Cu | ND1 B:His436 | 3.84 | Cu | CD2 B:His436 | 3.06 | Cu | CE1 B:His436 | 2.64 | Cu | CG B:His436 | 4.07 | Cu | CB B:Leu500 | 4.77 | Cu | CD1 B:Leu500 | 4.49 | Cu | NE2 B:His502 | 1.92 | Cu | ND1 B:His502 | 4.01 | Cu | CD2 B:His502 | 2.93 | Cu | CE1 B:His502 | 2.90 | Cu | CG B:His502 | 4.06 | Cu | CU B:Cu603 | 4.84 | Cu | CU B:Cu604 | 4.09 | Cu | O B:Hoh1087 | 4.42 | Cu | O B:Hoh1141 | 2.33 |
| interactive model:
| Copper binding site 7 out of 8 in 2ih9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Copper in the PDB 2ih9. 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: His93, B: His95, B: Trp136, B: His138, B: His434, B: His504, B: Cu602, B: Cu604, B: Hoh1087, B: Hoh1141, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 B:His93 | 4.23 | Cu | CD2 B:His93 | 3.81 | Cu | NE2 B:His95 | 3.99 | Cu | CB B:His95 | 3.53 | Cu | ND1 B:His95 | 1.96 | Cu | CD2 B:His95 | 4.13 | Cu | CE1 B:His95 | 2.83 | Cu | CG B:His95 | 3.08 | Cu | CA B:His95 | 4.67 | Cu | CZ2 B:Trp136 | 3.79 | Cu | CE2 B:Trp136 | 4.25 | Cu | NE1 B:Trp136 | 4.59 | Cu | CH2 B:Trp136 | 4.28 | Cu | NE2 B:His138 | 1.95 | Cu | ND1 B:His138 | 3.97 | Cu | CD2 B:His138 | 2.99 | Cu | CE1 B:His138 | 2.85 | Cu | CG B:His138 | 4.06 | Cu | NE2 B:His434 | 4.24 | Cu | CD2 B:His434 | 4.19 | Cu | CG B:His434 | 4.99 | Cu | NE2 B:His504 | 1.97 | Cu | ND1 B:His504 | 4.00 | Cu | CD2 B:His504 | 3.07 | Cu | CE1 B:His504 | 2.84 | Cu | CG B:His504 | 4.14 | Cu | CU B:Cu602 | 4.84 | Cu | CU B:Cu604 | 4.06 | Cu | O B:Hoh1087 | 4.67 | Cu | O B:Hoh1141 | 2.52 |
| interactive model:
| Copper binding site 8 out of 8 in 2ih9
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Copper in the PDB 2ih9. 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: His93, B: His95, B: Gly96, B: His434, B: Leu435, B: His436, B: Cu602, B: Cu603, B: Cl610, B: Hoh821, B: Hoh1141, | conact list:
Atom | Atom | Distance (A) | Cu | NE2 B:His93 | 1.91 | Cu | ND1 B:His93 | 3.94 | Cu | CD2 B:His93 | 3.02 | Cu | CE1 B:His93 | 2.78 | Cu | CG B:His93 | 4.09 | Cu | NE2 B:His95 | 4.65 | Cu | N B:His95 | 4.66 | Cu | CB B:His95 | 4.11 | Cu | ND1 B:His95 | 3.81 | Cu | CD2 B:His95 | 4.39 | Cu | C B:His95 | 4.73 | Cu | CE1 B:His95 | 4.33 | Cu | CG B:His95 | 3.85 | Cu | CA B:His95 | 3.81 | Cu | N B:Gly96 | 4.49 | Cu | NE2 B:His434 | 1.91 | Cu | ND1 B:His434 | 4.00 | Cu | CD2 B:His434 | 2.93 | Cu | CE1 B:His434 | 2.89 | Cu | CG B:His434 | 4.05 | Cu | O B:Leu435 | 4.73 | Cu | C B:Leu435 | 4.93 | Cu | NE2 B:His436 | 3.30 | Cu | N B:His436 | 4.83 | Cu | CB B:His436 | 4.62 | Cu | ND1 B:His436 | 4.18 | Cu | CD2 B:His436 | 3.16 | Cu | CE1 B:His436 | 3.94 | Cu | CG B:His436 | 3.76 | Cu | CA B:His436 | 4.43 | Cu | CU B:Cu602 | 4.09 | Cu | CU B:Cu603 | 4.06 | Cu | CL B:Cl610 | 2.76 | Cu | O B:Hoh821 | 4.86 | Cu | O B:Hoh1141 | 3.36 |
| interactive model:
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