Copper in the structure of Azurin Mutant M121A-Azide (pdb 2tsb)
The binding sites of Copper atom in the structure of Azurin Mutant M121A-Azide (pdb code 2tsb). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2tsb structure was solved by L.-C.TSAI, N.BONANDER, K.HARATA, B.G.KARLSSON, T.VANNGARD, V.LANGER, L.SJOLIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 8.0-2.3 | Space group | P212121 | a (A) | 109.700 | b (A) | 98.700 | c (A) | 48.100 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 19.4 | Rfree (%) | n/a |
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Copper Binding Sites:Copper binding site 1 out of 4 in 2tsb
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2tsb. 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: Gly45, A: His46, A: Asn47, A: Cys112, A: Phe114, A: His117, A: Ala121, A: Azi129, | conact list:
Atom | Atom | Distance (A) | Cu | O A:Gly45 | 3.14 | Cu | C A:Gly45 | 4.01 | Cu | NE2 A:His46 | 4.27 | Cu | N A:His46 | 4.06 | Cu | CB A:His46 | 3.49 | Cu | ND1 A:His46 | 2.19 | Cu | CD2 A:His46 | 4.32 | Cu | C A:His46 | 4.78 | Cu | CE1 A:His46 | 3.16 | Cu | CG A:His46 | 3.19 | Cu | CA A:His46 | 3.48 | Cu | N A:Asn47 | 4.87 | Cu | CB A:Cys112 | 3.55 | Cu | SG A:Cys112 | 2.37 | Cu | CA A:Cys112 | 4.97 | Cu | CB A:Phe114 | 4.29 | Cu | NE2 A:His117 | 4.52 | Cu | CB A:His117 | 3.70 | Cu | ND1 A:His117 | 2.45 | Cu | CD2 A:His117 | 4.58 | Cu | CE1 A:His117 | 3.37 | Cu | CG A:His117 | 3.46 | Cu | CB A:Ala121 | 4.52 | Cu | N1 A:Azi129 | 2.02 | Cu | N3 A:Azi129 | 3.95 | Cu | N2 A:Azi129 | 2.92 |
| interactive model:
| Copper binding site 2 out of 4 in 2tsb
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2tsb. 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: Gly45, B: His46, B: Asn47, B: Cys112, B: Phe114, B: His117, B: Ala121, B: Azi129, | conact list:
Atom | Atom | Distance (A) | Cu | O B:Gly45 | 3.16 | Cu | C B:Gly45 | 3.95 | Cu | NE2 B:His46 | 4.46 | Cu | N B:His46 | 3.96 | Cu | CB B:His46 | 2.99 | Cu | ND1 B:His46 | 2.31 | Cu | CD2 B:His46 | 4.25 | Cu | C B:His46 | 4.36 | Cu | CE1 B:His46 | 3.48 | Cu | CG B:His46 | 2.99 | Cu | CA B:His46 | 3.18 | Cu | N B:Asn47 | 4.46 | Cu | CB B:Cys112 | 3.52 | Cu | SG B:Cys112 | 2.33 | Cu | CA B:Cys112 | 4.93 | Cu | CB B:Phe114 | 4.22 | Cu | CG B:Phe114 | 4.85 | Cu | NE2 B:His117 | 4.41 | Cu | CB B:His117 | 3.42 | Cu | ND1 B:His117 | 2.31 | Cu | CD2 B:His117 | 4.39 | Cu | CE1 B:His117 | 3.33 | Cu | CG B:His117 | 3.22 | Cu | CA B:His117 | 4.91 | Cu | CB B:Ala121 | 4.70 | Cu | N1 B:Azi129 | 2.09 | Cu | N3 B:Azi129 | 4.06 | Cu | N2 B:Azi129 | 3.05 |
| interactive model:
| Copper binding site 3 out of 4 in 2tsb
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2tsb. 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: C: Gly45, C: His46, C: Asn47, C: Cys112, C: Phe114, C: His117, C: Ala121, C: Azi129, | conact list:
Atom | Atom | Distance (A) | Cu | O C:Gly45 | 3.14 | Cu | C C:Gly45 | 3.95 | Cu | NE2 C:His46 | 4.39 | Cu | N C:His46 | 4.13 | Cu | CB C:His46 | 3.62 | Cu | ND1 C:His46 | 2.33 | Cu | CD2 C:His46 | 4.44 | Cu | C C:His46 | 4.59 | Cu | CE1 C:His46 | 3.26 | Cu | CG C:His46 | 3.32 | Cu | CA C:His46 | 3.41 | Cu | N C:Asn47 | 4.62 | Cu | CB C:Cys112 | 3.15 | Cu | SG C:Cys112 | 2.23 | Cu | C C:Cys112 | 4.89 | Cu | CA C:Cys112 | 4.54 | Cu | CB C:Phe114 | 4.10 | Cu | CG C:Phe114 | 4.91 | Cu | NE2 C:His117 | 4.41 | Cu | CB C:His117 | 3.27 | Cu | ND1 C:His117 | 2.33 | Cu | CD2 C:His117 | 4.33 | Cu | CE1 C:His117 | 3.38 | Cu | CG C:His117 | 3.14 | Cu | CA C:His117 | 4.71 | Cu | CB C:Ala121 | 4.61 | Cu | N1 C:Azi129 | 2.00 | Cu | N3 C:Azi129 | 4.10 | Cu | N2 C:Azi129 | 3.01 |
| interactive model:
| Copper binding site 4 out of 4 in 2tsb
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2tsb. 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: D: Gly45, D: His46, D: Asn47, D: Cys112, D: Phe114, D: His117, D: Ala121, D: Azi129, | conact list:
Atom | Atom | Distance (A) | Cu | O D:Gly45 | 3.28 | Cu | C D:Gly45 | 4.06 | Cu | NE2 D:His46 | 4.26 | Cu | N D:His46 | 4.09 | Cu | CB D:His46 | 3.32 | Cu | ND1 D:His46 | 2.17 | Cu | CD2 D:His46 | 4.23 | Cu | C D:His46 | 4.52 | Cu | CE1 D:His46 | 3.19 | Cu | CG D:His46 | 3.07 | Cu | CA D:His46 | 3.36 | Cu | N D:Asn47 | 4.64 | Cu | CB D:Cys112 | 3.45 | Cu | SG D:Cys112 | 2.37 | Cu | CA D:Cys112 | 4.90 | Cu | CB D:Phe114 | 4.32 | Cu | NE2 D:His117 | 4.34 | Cu | CB D:His117 | 3.99 | Cu | ND1 D:His117 | 2.41 | Cu | CD2 D:His117 | 4.50 | Cu | CE1 D:His117 | 3.14 | Cu | CG D:His117 | 3.51 | Cu | CB D:Ala121 | 4.64 | Cu | N1 D:Azi129 | 2.07 | Cu | N3 D:Azi129 | 4.23 | Cu | N2 D:Azi129 | 3.11 |
| interactive model:
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