Copper in the structure of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase (pdb 3s0p)

The binding sites of Copper atom in the structure of Copper-Reconstituted Tomato Chloroplast Superoxide Dismutase (pdb code 3s0p). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 3s0p structure was solved by A.GALALELDEEN, A.B.TAYLOR, P.J.HART, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.7-3.0 Space group P1211 a (A) 66.866 b (A) 105.329 c (A) 69.660 alpha (°) 90.00 beta (°) 96.43 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 24.9 Copper Binding Sites: Copper binding site 1 out of 8 in 3s0p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 3s0p. 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: His46, A: His48, A: His63, A: Val118, A: His120, conact list: Atom Atom Distance (A) Cu NE2 A:His46 4.44 Cu N A:His46 4.82 Cu CB A:His46 3.03 Cu ND1 A:His46 2.33 Cu CD2 A:His46 4.27 Cu CE1 A:His46 3.47 Cu CG A:His46 3.02 Cu CA A:His46 4.42 Cu NE2 A:His48 2.17 Cu ND1 A:His48 4.13 Cu CD2 A:His48 3.29 Cu CE1 A:His48 2.97 Cu CG A:His48 4.33 Cu NE2 A:His63 3.68 Cu ND1 A:His63 4.42 Cu CD2 A:His63 4.49 Cu CE1 A:His63 3.65 Cu CG A:His63 4.91 Cu O A:Val118 4.93 Cu CB A:Val118 4.39 Cu CG1 A:Val118 4.39 Cu NE2 A:His120 2.80 Cu ND1 A:His120 3.42 Cu CD2 A:His120 3.98 Cu CE1 A:His120 2.36 Cu CG A:His120 4.29 interactive model: Copper binding site 2 out of 8 in 3s0p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 3s0p. 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: His46, B: His48, B: His63, B: Val118, B: His120, conact list: Atom Atom Distance (A) Cu NE2 B:His46 4.48 Cu N B:His46 4.80 Cu CB B:His46 3.06 Cu ND1 B:His46 2.38 Cu CD2 B:His46 4.30 Cu CE1 B:His46 3.51 Cu CG B:His46 3.05 Cu CA B:His46 4.45 Cu NE2 B:His48 2.14 Cu ND1 B:His48 4.11 Cu CD2 B:His48 3.25 Cu CE1 B:His48 2.95 Cu CG B:His48 4.31 Cu NE2 B:His63 3.68 Cu ND1 B:His63 4.45 Cu CD2 B:His63 4.50 Cu CE1 B:His63 3.68 Cu CG B:His63 4.94 Cu O B:Val118 4.75 Cu CB B:Val118 4.32 Cu CG1 B:Val118 4.42 Cu NE2 B:His120 2.84 Cu ND1 B:His120 3.35 Cu CD2 B:His120 4.04 Cu CE1 B:His120 2.30 Cu CG B:His120 4.28 interactive model: Copper binding site 3 out of 8 in 3s0p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 3s0p. 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: His46, C: His48, C: His63, C: Val118, C: His120, conact list: Atom Atom Distance (A) Cu NE2 C:His46 4.38 Cu N C:His46 4.87 Cu CB C:His46 3.02 Cu ND1 C:His46 2.29 Cu CD2 C:His46 4.21 Cu CE1 C:His46 3.42 Cu CG C:His46 2.97 Cu CA C:His46 4.44 Cu NE2 C:His48 2.20 Cu ND1 C:His48 4.12 Cu CD2 C:His48 3.32 Cu CE1 C:His48 2.97 Cu CG C:His48 4.34 Cu NE2 C:His63 3.52 Cu ND1 C:His63 4.30 Cu CD2 C:His63 4.31 Cu CE1 C:His63 3.55 Cu CG C:His63 4.75 Cu O C:Val118 4.99 Cu CB C:Val118 4.51 Cu CG1 C:Val118 4.62 Cu NE2 C:His120 2.85 Cu ND1 C:His120 3.49 Cu CD2 C:His120 4.06 Cu CE1 C:His120 2.41 Cu CG C:His120 4.36 interactive model: Copper binding site 4 out of 8 in 3s0p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 3s0p. 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: His46, D: His48, D: His63, D: Val118, D: His120, conact list: Atom Atom Distance (A) Cu NE2 D:His46 4.39 Cu N D:His46 4.83 Cu CB D:His46 3.07 Cu ND1 D:His46 2.30 Cu CD2 D:His46 4.23 Cu CE1 D:His46 3.42 Cu CG D:His46 3.01 Cu CA D:His46 4.46 Cu NE2 D:His48 2.17 Cu ND1 D:His48 4.14 Cu CD2 D:His48 3.29 Cu CE1 D:His48 2.97 Cu CG D:His48 4.34 Cu NE2 D:His63 3.57 Cu ND1 D:His63 4.46 Cu CD2 D:His63 4.35 Cu CE1 D:His63 3.67 Cu CG D:His63 4.85 Cu O D:Val118 4.98 Cu CB D:Val118 4.46 Cu CG1 D:Val118 4.45 Cu NE2 D:His120 2.77 Cu ND1 D:His120 3.43 Cu CD2 D:His120 3.97 Cu CE1 D:His120 2.36 Cu CG D:His120 4.29 interactive model: Copper binding site 5 out of 8 in 3s0p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 3s0p. 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: His46, E: His48, E: His63, E: Val118, E: His120, conact list: Atom Atom Distance (A) Cu NE2 E:His46 4.48 Cu CB E:His46 3.29 Cu ND1 E:His46 2.43 Cu CD2 E:His46 4.37 Cu CE1 E:His46 3.48 Cu CG E:His46 3.18 Cu CA E:His46 4.70 Cu NE2 E:His48 2.21 Cu ND1 E:His48 4.05 Cu CD2 E:His48 3.42 Cu CE1 E:His48 2.84 Cu CG E:His48 4.37 Cu NE2 E:His63 3.41 Cu ND1 E:His63 4.36 Cu CD2 E:His63 4.24 Cu CE1 E:His63 3.53 Cu CG E:His63 4.77 Cu CB E:Val118 4.64 Cu CG1 E:Val118 4.55 Cu NE2 E:His120 2.69 Cu ND1 E:His120 3.53 Cu CD2 E:His120 3.90 Cu CE1 E:His120 2.41 Cu CG E:His120 4.31 interactive model: Copper binding site 6 out of 8 in 3s0p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 3s0p. 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: F: His46, F: His48, F: His63, F: Val118, F: His120, conact list: Atom Atom Distance (A) Cu NE2 F:His46 4.38 Cu N F:His46 4.76 Cu CB F:His46 3.01 Cu ND1 F:His46 2.26 Cu CD2 F:His46 4.21 Cu C F:His46 5.00 Cu CE1 F:His46 3.41 Cu CG F:His46 2.97 Cu CA F:His46 4.40 Cu NE2 F:His48 2.21 Cu ND1 F:His48 4.21 Cu CD2 F:His48 3.30 Cu CE1 F:His48 3.05 Cu CG F:His48 4.38 Cu NE2 F:His63 3.71 Cu ND1 F:His63 4.51 Cu CD2 F:His63 4.53 Cu CE1 F:His63 3.73 Cu CG F:His63 4.97 Cu O F:Val118 4.82 Cu CB F:Val118 4.39 Cu CG1 F:Val118 4.35 Cu NE2 F:His120 2.73 Cu ND1 F:His120 3.30 Cu CD2 F:His120 3.91 Cu CE1 F:His120 2.25 Cu CG F:His120 4.18 interactive model: Copper binding site 7 out of 8 in 3s0p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Copper in the PDB 3s0p. 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: His46, G: His48, G: His63, G: Val118, G: His120, conact list: Atom Atom Distance (A) Cu NE2 G:His46 4.41 Cu N G:His46 4.75 Cu CB G:His46 3.16 Cu ND1 G:His46 2.29 Cu CD2 G:His46 4.29 Cu CE1 G:His46 3.40 Cu CG G:His46 3.07 Cu CA G:His46 4.49 Cu NE2 G:His48 2.27 Cu ND1 G:His48 4.27 Cu CD2 G:His48 3.38 Cu CE1 G:His48 3.09 Cu CG G:His48 4.46 Cu NE2 G:His63 3.83 Cu ND1 G:His63 4.65 Cu CD2 G:His63 4.67 Cu CE1 G:His63 3.85 Cu O G:Val118 4.80 Cu CB G:Val118 4.31 Cu CG1 G:Val118 4.34 Cu NE2 G:His120 2.71 Cu ND1 G:His120 3.08 Cu CD2 G:His120 3.93 Cu CE1 G:His120 2.03 Cu CG G:His120 4.06 interactive model: Copper binding site 8 out of 8 in 3s0p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Copper in the PDB 3s0p. 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: H: His46, H: His48, H: His63, H: Val118, H: His120, conact list: Atom Atom Distance (A) Cu NE2 H:His46 4.44 Cu CB H:His46 3.14 Cu ND1 H:His46 2.35 Cu CD2 H:His46 4.30 Cu CE1 H:His46 3.45 Cu CG H:His46 3.08 Cu CA H:His46 4.58 Cu NE2 H:His48 2.21 Cu ND1 H:His48 4.13 Cu CD2 H:His48 3.36 Cu CE1 H:His48 2.94 Cu CG H:His48 4.38 Cu NE2 H:His63 3.50 Cu ND1 H:His63 4.40 Cu CD2 H:His63 4.31 Cu CE1 H:His63 3.60 Cu CG H:His63 4.83 Cu CB H:Val118 4.54 Cu CG1 H:Val118 4.52 Cu NE2 H:His120 2.70 Cu ND1 H:His120 3.45 Cu CD2 H:His120 3.91 Cu CE1 H:His120 2.34 Cu CG H:His120 4.28 interactive model: