The binding sites of Copper atom in the structure of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Oxidized Form (pdb code 1n5w). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1n5w structure was solved by H.DOBBEK, L.GREMER, R.KIEFERSAUER, R.HUBER, O.MEYER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 18.0-1.5 | Space group | P212121 | a (A) | 119.295 | b (A) | 132.088 | c (A) | 159.825 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 13.5 | Rfree (%) | 17.1 |
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Copper binding site 1 out of 2 in 1n5w
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1n5w. 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: Val384, B: Ala385, B: Tyr386, B: Arg387, B: Cys388, B: Ser389, B: Phe390, B: Glu763, B: Cum3921, B: Hoh4334, B: Hoh4547, | conact list:
Atom | Atom | Distance (A) | Cu | O B:Val384 | 4.77 | Cu | CB B:Val384 | 4.78 | Cu | C B:Val384 | 4.05 | Cu | CG1 B:Val384 | 3.83 | Cu | CA B:Val384 | 4.60 | Cu | O B:Ala385 | 3.75 | Cu | N B:Ala385 | 3.44 | Cu | C B:Ala385 | 3.60 | Cu | CA B:Ala385 | 3.63 | Cu | N B:Tyr386 | 4.22 | Cu | C B:Tyr386 | 4.78 | Cu | N B:Arg387 | 4.18 | Cu | C B:Arg387 | 4.23 | Cu | CA B:Arg387 | 4.49 | Cu | O B:Cys388 | 4.91 | Cu | N B:Cys388 | 3.15 | Cu | CB B:Cys388 | 3.29 | Cu | SG B:Cys388 | 2.22 | Cu | C B:Cys388 | 3.88 | Cu | CA B:Cys388 | 3.54 | Cu | N B:Ser389 | 3.52 | Cu | C B:Ser389 | 4.91 | Cu | CA B:Ser389 | 4.53 | Cu | N B:Phe390 | 4.19 | Cu | OE2 B:Glu763 | 3.67 | Cu | CD B:Glu763 | 4.92 | Cu | S B:Cum3921 | 2.21 | Cu | OM1 B:Cum3921 | 4.87 | Cu | MO B:Cum3921 | 3.75 | Cu | OM2 B:Cum3921 | 3.37 | Cu | CU B:Cum3921 | 0.00 | Cu | O B:Hoh4334 | 2.42 | Cu | O B:Hoh4547 | 4.56 |
| interactive model:
| Copper binding site 2 out of 2 in 1n5w
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1n5w. 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: E: Val384, E: Ala385, E: Tyr386, E: Arg387, E: Cys388, E: Ser389, E: Phe390, E: Glu763, E: Cum4921, E: Hoh5313, | conact list:
Atom | Atom | Distance (A) | Cu | O E:Val384 | 4.74 | Cu | CB E:Val384 | 4.77 | Cu | C E:Val384 | 4.08 | Cu | CG1 E:Val384 | 3.81 | Cu | CA E:Val384 | 4.59 | Cu | O E:Ala385 | 3.73 | Cu | N E:Ala385 | 3.41 | Cu | C E:Ala385 | 3.63 | Cu | CA E:Ala385 | 3.62 | Cu | N E:Tyr386 | 4.19 | Cu | C E:Tyr386 | 4.84 | Cu | N E:Arg387 | 4.23 | Cu | C E:Arg387 | 4.25 | Cu | CA E:Arg387 | 4.51 | Cu | O E:Cys388 | 4.92 | Cu | N E:Cys388 | 3.14 | Cu | CB E:Cys388 | 3.32 | Cu | SG E:Cys388 | 2.22 | Cu | C E:Cys388 | 3.92 | Cu | CA E:Cys388 | 3.56 | Cu | N E:Ser389 | 3.55 | Cu | C E:Ser389 | 4.89 | Cu | CA E:Ser389 | 4.54 | Cu | N E:Phe390 | 4.16 | Cu | OE2 E:Glu763 | 3.70 | Cu | CD E:Glu763 | 4.93 | Cu | S E:Cum4921 | 2.21 | Cu | OM1 E:Cum4921 | 4.91 | Cu | MO E:Cum4921 | 3.74 | Cu | OM2 E:Cum4921 | 3.36 | Cu | CU E:Cum4921 | 0.00 | Cu | O E:Hoh5313 | 2.49 |
| interactive model:
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