Copper in the structure of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu,Zn Enzyme Superoxide Dismutase (pdb 1sdy)

The binding sites of Copper atom in the structure of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu,Zn Enzyme Superoxide Dismutase (pdb code 1sdy). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1sdy structure was solved by K.DJINOVIC, G.GATTI, A.CODA, L.ANTOLINI, G.PELOSI, A.DESIDERI, M.FALCONI, F.MARMOCCHI, G.ROTILIO, M.BOLOGNESI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.5 Space group P21212 a (A) 105.300 b (A) 143.000 c (A) 62.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Copper Binding Sites: Copper binding site 1 out of 4 in 1sdy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1sdy. 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: His44, A: His46, A: His61, A: Val116, A: His118, A: Hoh154, A: Hoh273, conact list: Atom Atom Distance (A) Cu NE2 A:His44 3.99 Cu N A:His44 4.76 Cu CB A:His44 3.16 Cu ND1 A:His44 1.85 Cu CD2 A:His44 3.99 Cu CE1 A:His44 2.89 Cu CG A:His44 2.84 Cu CA A:His44 4.56 Cu NE2 A:His46 2.17 Cu ND1 A:His46 4.25 Cu CD2 A:His46 3.17 Cu CE1 A:His46 3.10 Cu CG A:His46 4.27 Cu NE2 A:His61 2.44 Cu ND1 A:His61 4.57 Cu CD2 A:His61 3.06 Cu CE1 A:His61 3.60 Cu CG A:His61 4.30 Cu CG2 A:Val116 4.71 Cu CG1 A:Val116 4.97 Cu NE2 A:His118 2.24 Cu ND1 A:His118 4.34 Cu CD2 A:His118 3.23 Cu CE1 A:His118 3.19 Cu CG A:His118 4.35 Cu O A:Hoh154 1.86 Cu O A:Hoh273 4.52 interactive model: Copper binding site 2 out of 4 in 1sdy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1sdy. 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, B: Hoh226, conact list: Atom Atom Distance (A) Cu NE2 B:His44 3.99 Cu N B:His44 4.87 Cu CB B:His44 3.18 Cu ND1 B:His44 1.87 Cu CD2 B:His44 4.01 Cu CE1 B:His44 2.89 Cu CG B:His44 2.87 Cu CA B:His44 4.59 Cu NE2 B:His46 2.28 Cu ND1 B:His46 4.33 Cu CD2 B:His46 3.33 Cu CE1 B:His46 3.15 Cu CG B:His46 4.40 Cu NE2 B:His61 2.08 Cu ND1 B:His61 4.24 Cu CD2 B:His61 2.83 Cu CE1 B:His61 3.25 Cu CG B:His61 4.06 Cu CG2 B:Val116 4.67 Cu NE2 B:His118 2.01 Cu ND1 B:His118 3.99 Cu CD2 B:His118 3.13 Cu CE1 B:His118 2.81 Cu CG B:His118 4.15 Cu O B:Hoh154 2.06 Cu O B:Hoh226 4.95 interactive model: Copper binding site 3 out of 4 in 1sdy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1sdy. 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: His44, C: His46, C: His61, C: Val116, C: His118, C: Hoh154, C: Hoh240, conact list: Atom Atom Distance (A) Cu NE2 C:His44 3.99 Cu N C:His44 4.75 Cu CB C:His44 3.40 Cu ND1 C:His44 1.91 Cu CD2 C:His44 4.11 Cu CE1 C:His44 2.82 Cu CG C:His44 3.00 Cu CA C:His44 4.63 Cu NE2 C:His46 2.30 Cu ND1 C:His46 4.40 Cu CD2 C:His46 3.26 Cu CE1 C:His46 3.25 Cu CG C:His46 4.40 Cu NE2 C:His61 2.00 Cu ND1 C:His61 4.13 Cu CD2 C:His61 2.94 Cu CE1 C:His61 3.03 Cu CG C:His61 4.10 Cu CB C:Val116 4.83 Cu CG1 C:Val116 4.91 Cu NE2 C:His118 2.14 Cu ND1 C:His118 4.15 Cu CD2 C:His118 3.17 Cu CE1 C:His118 3.01 Cu CG C:His118 4.21 Cu O C:Hoh154 1.83 Cu O C:Hoh240 4.21 interactive model: Copper binding site 4 out of 4 in 1sdy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1sdy. 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: His44, D: His46, D: His61, D: Val116, D: His118, D: Hoh154, D: Hoh255, conact list: Atom Atom Distance (A) Cu NE2 D:His44 3.92 Cu N D:His44 4.87 Cu CB D:His44 3.33 Cu ND1 D:His44 1.82 Cu CD2 D:His44 4.01 Cu CE1 D:His44 2.77 Cu CG D:His44 2.90 Cu CA D:His44 4.64 Cu NE2 D:His46 2.13 Cu ND1 D:His46 4.21 Cu CD2 D:His46 3.10 Cu CE1 D:His46 3.12 Cu CG D:His46 4.20 Cu NE2 D:His61 2.16 Cu ND1 D:His61 4.33 Cu CD2 D:His61 2.94 Cu CE1 D:His61 3.29 Cu CG D:His61 4.15 Cu CB D:Val116 4.75 Cu CG1 D:Val116 4.73 Cu NE2 D:His118 2.26 Cu ND1 D:His118 4.37 Cu CD2 D:His118 3.29 Cu CE1 D:His118 3.19 Cu CG D:His118 4.39 Cu O D:Hoh154 2.37 Cu O D:Hoh255 4.88 interactive model: