Copper in the structure of Determination and Analysis Of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase (pdb 2sod)

The binding sites of Copper atom in the structure of Determination and Analysis Of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase (pdb code 2sod). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2sod structure was solved by J.A.TAINER, E.D.GETZOFF, J.S.RICHARDSON, D.C.RICHARDSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 2.0 Space group C121 a (A) 93.650 b (A) 90.330 c (A) 71.650 alpha (°) 90.00 beta (°) 95.10 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Copper Binding Sites: Copper binding site 1 out of 4 in 2sod Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2sod. 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: O: His44, O: His46, O: His61, O: Val116, O: His118, O: Hoh154, conact list: Atom Atom Distance (A) Cu NE2 O:His44 4.08 Cu CB O:His44 3.19 Cu ND1 O:His44 2.01 Cu CD2 O:His44 4.06 Cu CE1 O:His44 3.03 Cu CG O:His44 2.93 Cu CA O:His44 4.79 Cu NE2 O:His46 2.11 Cu ND1 O:His46 4.11 Cu CD2 O:His46 3.23 Cu CE1 O:His46 2.93 Cu CG O:His46 4.29 Cu NE2 O:His61 2.21 Cu ND1 O:His61 4.32 Cu CD2 O:His61 3.11 Cu CE1 O:His61 3.25 Cu CG O:His61 4.28 Cu CG1 O:Val116 3.98 Cu NE2 O:His118 2.10 Cu ND1 O:His118 4.05 Cu CD2 O:His118 3.08 Cu CE1 O:His118 2.98 Cu CG O:His118 4.11 Cu O O:Hoh154 3.20 interactive model: Copper binding site 2 out of 4 in 2sod Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2sod. 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: Y: His44, Y: His46, Y: His61, Y: Val116, Y: His118, Y: Thr135, Y: Hoh154, conact list: Atom Atom Distance (A) Cu O Y:His44 4.98 Cu NE2 Y:His44 4.03 Cu N Y:His44 4.97 Cu CB Y:His44 3.27 Cu ND1 Y:His44 1.96 Cu CD2 Y:His44 4.07 Cu CE1 Y:His44 2.97 Cu CG Y:His44 2.95 Cu CA Y:His44 4.68 Cu NE2 Y:His46 2.12 Cu ND1 Y:His46 4.12 Cu CD2 Y:His46 3.19 Cu CE1 Y:His46 2.98 Cu CG Y:His46 4.30 Cu NE2 Y:His61 1.98 Cu ND1 Y:His61 4.09 Cu CD2 Y:His61 3.01 Cu CE1 Y:His61 2.93 Cu CG Y:His61 4.14 Cu CG1 Y:Val116 3.81 Cu NE2 Y:His118 1.99 Cu ND1 Y:His118 4.02 Cu CD2 Y:His118 3.00 Cu CE1 Y:His118 2.92 Cu CG Y:His118 4.10 Cu O Y:Thr135 4.80 Cu O Y:Hoh154 2.49 interactive model: Copper binding site 3 out of 4 in 2sod Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2sod. 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: His44, B: His46, B: His61, B: Val116, B: His118, B: Hoh154, conact list: Atom Atom Distance (A) Cu O B:His44 4.96 Cu NE2 B:His44 4.03 Cu N B:His44 4.63 Cu CB B:His44 3.48 Cu ND1 B:His44 2.00 Cu CD2 B:His44 4.12 Cu C B:His44 4.92 Cu CE1 B:His44 2.93 Cu CG B:His44 3.02 Cu CA B:His44 4.56 Cu NE2 B:His46 2.15 Cu ND1 B:His46 4.16 Cu CD2 B:His46 3.20 Cu CE1 B:His46 3.00 Cu CG B:His46 4.31 Cu NE2 B:His61 2.26 Cu ND1 B:His61 4.27 Cu CD2 B:His61 3.08 Cu CE1 B:His61 3.26 Cu CG B:His61 4.23 Cu CB B:Val116 4.77 Cu CG1 B:Val116 3.97 Cu NE2 B:His118 1.98 Cu ND1 B:His118 4.01 Cu CD2 B:His118 2.95 Cu CE1 B:His118 2.94 Cu CG B:His118 4.08 Cu O B:Hoh154 3.90 interactive model: Copper binding site 4 out of 4 in 2sod Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2sod. 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: G: His44, G: His46, G: His61, G: Val116, G: His118, G: Hoh154, conact list: Atom Atom Distance (A) Cu NE2 G:His44 3.95 Cu N G:His44 4.71 Cu CB G:His44 3.18 Cu ND1 G:His44 2.06 Cu CD2 G:His44 3.94 Cu C G:His44 4.99 Cu CE1 G:His44 2.98 Cu CG G:His44 2.91 Cu CA G:His44 4.53 Cu NE2 G:His46 2.02 Cu ND1 G:His46 3.98 Cu CD2 G:His46 2.98 Cu CE1 G:His46 2.92 Cu CG G:His46 4.07 Cu NE2 G:His61 2.21 Cu ND1 G:His61 4.32 Cu CD2 G:His61 2.97 Cu CE1 G:His61 3.31 Cu CG G:His61 4.21 Cu CG2 G:Val116 4.78 Cu CG1 G:Val116 4.64 Cu NE2 G:His118 2.07 Cu ND1 G:His118 4.12 Cu CD2 G:His118 3.09 Cu CE1 G:His118 3.00 Cu CG G:His118 4.21 Cu O G:Hoh154 3.83 interactive model: