Copper in the structure of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase (pdb 1sda)

The binding sites of Copper atom in the structure of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase (pdb code 1sda). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1sda structure was solved by C.D.SMITH, M.CARSON, M.VAN DER WOERD, J.CHEN, H.ISCHIROPOULOS, J.S.BECKMAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 2.5 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 (%) 18.7 Rfree (%) n/a Copper Binding Sites: Copper binding site 1 out of 4 in 1sda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1sda. 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: Hoh803, conact list: Atom Atom Distance (A) Cu O O:His44 4.81 Cu NE2 O:His44 4.11 Cu N O:His44 4.46 Cu CB O:His44 2.75 Cu ND1 O:His44 1.96 Cu CD2 O:His44 3.90 Cu C O:His44 4.78 Cu CE1 O:His44 3.14 Cu CG O:His44 2.65 Cu CA O:His44 4.13 Cu NE2 O:His46 2.18 Cu ND1 O:His46 4.25 Cu CD2 O:His46 3.15 Cu CE1 O:His46 3.10 Cu CG O:His46 4.28 Cu NE2 O:His61 2.37 Cu ND1 O:His61 4.42 Cu CD2 O:His61 3.07 Cu CE1 O:His61 3.43 Cu CG O:His61 4.26 Cu CB O:Val116 4.73 Cu NE2 O:His118 2.14 Cu ND1 O:His118 4.22 Cu CD2 O:His118 2.92 Cu CE1 O:His118 3.17 Cu CG O:His118 4.10 Cu O O:Hoh803 4.92 interactive model: Copper binding site 2 out of 4 in 1sda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1sda. 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: Hoh806, conact list: Atom Atom Distance (A) Cu O Y:His44 4.95 Cu NE2 Y:His44 3.94 Cu N Y:His44 4.63 Cu CB Y:His44 3.02 Cu ND1 Y:His44 1.83 Cu CD2 Y:His44 3.89 Cu C Y:His44 4.96 Cu CE1 Y:His44 2.88 Cu CG Y:His44 2.73 Cu CA Y:His44 4.35 Cu NE2 Y:His46 2.32 Cu ND1 Y:His46 4.33 Cu CD2 Y:His46 3.35 Cu CE1 Y:His46 3.14 Cu CG Y:His46 4.44 Cu NE2 Y:His61 2.05 Cu ND1 Y:His61 4.17 Cu CD2 Y:His61 2.78 Cu CE1 Y:His61 3.17 Cu CG Y:His61 4.00 Cu CB Y:Val116 4.98 Cu CG1 Y:Val116 4.92 Cu NE2 Y:His118 1.99 Cu ND1 Y:His118 3.99 Cu CD2 Y:His118 3.02 Cu CE1 Y:His118 2.83 Cu CG Y:His118 4.09 Cu O Y:Thr135 4.94 Cu O Y:Hoh806 4.72 interactive model: Copper binding site 3 out of 4 in 1sda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1sda. 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: Hoh809, conact list: Atom Atom Distance (A) Cu NE2 B:His44 4.01 Cu N B:His44 4.78 Cu CB B:His44 3.07 Cu ND1 B:His44 1.93 Cu CD2 B:His44 3.94 Cu CE1 B:His44 2.97 Cu CG B:His44 2.79 Cu CA B:His44 4.47 Cu NE2 B:His46 2.11 Cu ND1 B:His46 4.01 Cu CD2 B:His46 3.24 Cu CE1 B:His46 2.79 Cu CG B:His46 4.23 Cu NE2 B:His61 2.25 Cu ND1 B:His61 4.37 Cu CD2 B:His61 2.85 Cu CE1 B:His61 3.43 Cu CG B:His61 4.12 Cu CB B:Val116 4.84 Cu CG1 B:Val116 4.64 Cu NE2 B:His118 2.02 Cu ND1 B:His118 4.06 Cu CD2 B:His118 2.95 Cu CE1 B:His118 2.95 Cu CG B:His118 4.07 Cu O B:Hoh809 4.58 interactive model: Copper binding site 4 out of 4 in 1sda Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1sda. 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, conact list: Atom Atom Distance (A) Cu NE2 G:His44 3.78 Cu N G:His44 4.58 Cu CB G:His44 3.17 Cu ND1 G:His44 1.78 Cu CD2 G:His44 3.82 Cu C G:His44 4.95 Cu CE1 G:His44 2.71 Cu CG G:His44 2.75 Cu CA G:His44 4.40 Cu NE2 G:His46 2.12 Cu ND1 G:His46 4.15 Cu CD2 G:His46 3.14 Cu CE1 G:His46 2.98 Cu CG G:His46 4.24 Cu NE2 G:His61 2.20 Cu ND1 G:His61 4.25 Cu CD2 G:His61 2.68 Cu CE1 G:His61 3.38 Cu CG G:His61 3.94 Cu CB G:Val116 4.72 Cu CG1 G:Val116 4.88 Cu NE2 G:His118 2.15 Cu ND1 G:His118 4.11 Cu CD2 G:His118 3.22 Cu CE1 G:His118 2.91 Cu CG G:His118 4.26 interactive model: