Copper in the structure of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex With Phenylthiourea (Ptu) (pdb 1bug)

The binding sites of Copper atom in the structure of Catechol Oxidase From Ipomoea Batatas (Sweet Potatoes)- Inhibitor Complex With Phenylthiourea (Ptu) (pdb code 1bug). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1bug structure was solved by T.KLABUNDE, C.EICKEN, J.C.SACCHETTINI, B.KREBS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.7 Space group P1211 a (A) 45.820 b (A) 164.750 c (A) 52.160 alpha (°) 90.00 beta (°) 97.50 gamma (°) 90.00 Rfactor (%) 18.1 Rfree (%) 27.3 Copper Binding Sites: Copper binding site 1 out of 4 in 1bug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1bug. 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: His88, A: Cys92, A: His109, A: Phe114, A: Phe117, A: His118, A: Phe270, A: His274, A: Cu501, A: Urs1002, conact list: Atom Atom Distance (A) Cu NE2 A:His88 2.03 Cu ND1 A:His88 4.13 Cu CD2 A:His88 2.92 Cu CE1 A:His88 3.07 Cu CG A:His88 4.09 Cu SG A:Cys92 3.97 Cu NE2 A:His109 2.25 Cu ND1 A:His109 4.37 Cu CD2 A:His109 3.08 Cu CE1 A:His109 3.33 Cu CG A:His109 4.28 Cu CE1 A:Phe114 4.92 Cu CE2 A:Phe117 4.72 Cu CD2 A:Phe117 4.72 Cu NE2 A:His118 2.19 Cu ND1 A:His118 4.16 Cu CD2 A:His118 3.10 Cu CE1 A:His118 3.11 Cu CG A:His118 4.19 Cu CE2 A:Phe270 4.53 Cu CZ A:Phe270 4.35 Cu NE2 A:His274 4.58 Cu CE1 A:His274 4.31 Cu CU A:Cu501 4.25 Cu S1 A:Urs1002 2.26 Cu N1 A:Urs1002 4.58 Cu N2 A:Urs1002 3.22 Cu C7 A:Urs1002 3.19 interactive model: Copper binding site 2 out of 4 in 1bug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1bug. 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: His88, A: His240, A: His244, A: Phe270, A: His273, A: His274, A: Cu500, A: Urs1002, conact list: Atom Atom Distance (A) Cu NE2 A:His88 4.79 Cu CE1 A:His88 4.97 Cu O A:His240 4.95 Cu NE2 A:His240 2.14 Cu ND1 A:His240 4.15 Cu CD2 A:His240 3.17 Cu CE1 A:His240 3.02 Cu CG A:His240 4.25 Cu NE2 A:His244 2.05 Cu ND1 A:His244 3.85 Cu CD2 A:His244 3.01 Cu CE1 A:His244 2.80 Cu CG A:His244 3.98 Cu CE2 A:Phe270 3.84 Cu CD2 A:Phe270 4.41 Cu CZ A:Phe270 4.67 Cu ND1 A:His273 4.94 Cu NE2 A:His274 2.14 Cu ND1 A:His274 4.20 Cu CD2 A:His274 3.11 Cu CE1 A:His274 3.11 Cu CG A:His274 4.24 Cu CU A:Cu500 4.25 Cu S1 A:Urs1002 2.33 Cu N1 A:Urs1002 2.58 Cu N2 A:Urs1002 3.97 Cu C7 A:Urs1002 2.72 Cu C4 A:Urs1002 3.99 Cu C3 A:Urs1002 3.48 Cu C2 A:Urs1002 4.50 interactive model: Copper binding site 3 out of 4 in 1bug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1bug. 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: His88, B: Cys92, B: His109, B: Phe114, B: Phe117, B: His118, B: Phe270, B: His274, B: Cu501, B: Urs1002, conact list: Atom Atom Distance (A) Cu NE2 B:His88 2.21 Cu ND1 B:His88 4.31 Cu CD2 B:His88 3.02 Cu CE1 B:His88 3.29 Cu CG B:His88 4.22 Cu SG B:Cys92 3.92 Cu NE2 B:His109 2.22 Cu ND1 B:His109 4.35 Cu CD2 B:His109 3.02 Cu CE1 B:His109 3.32 Cu CG B:His109 4.24 Cu CE1 B:Phe114 4.75 Cu CE2 B:Phe117 4.68 Cu CD2 B:Phe117 4.68 Cu NE2 B:His118 2.10 Cu ND1 B:His118 4.06 Cu CD2 B:His118 3.02 Cu CE1 B:His118 3.01 Cu CG B:His118 4.11 Cu CE2 B:Phe270 4.61 Cu CZ B:Phe270 4.43 Cu NE2 B:His274 4.54 Cu CE1 B:His274 4.31 Cu CU B:Cu501 4.19 Cu S1 B:Urs1002 2.22 Cu N1 B:Urs1002 4.66 Cu N2 B:Urs1002 3.38 Cu C7 B:Urs1002 3.28 interactive model: Copper binding site 4 out of 4 in 1bug Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1bug. 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: His88, B: Phe114, B: His240, B: His244, B: Phe270, B: His273, B: His274, B: Cu500, B: Urs1002, conact list: Atom Atom Distance (A) Cu NE2 B:His88 4.76 Cu CE1 B:His88 5.00 Cu CE1 B:Phe114 4.80 Cu O B:His240 4.82 Cu NE2 B:His240 2.04 Cu ND1 B:His240 4.06 Cu CD2 B:His240 3.08 Cu CE1 B:His240 2.93 Cu CG B:His240 4.16 Cu NE2 B:His244 2.08 Cu ND1 B:His244 4.04 Cu CD2 B:His244 3.00 Cu CE1 B:His244 2.99 Cu CG B:His244 4.08 Cu CE2 B:Phe270 4.04 Cu CD2 B:Phe270 4.59 Cu CZ B:Phe270 4.82 Cu ND1 B:His273 4.97 Cu NE2 B:His274 2.13 Cu ND1 B:His274 4.16 Cu CD2 B:His274 3.18 Cu CE1 B:His274 3.02 Cu CG B:His274 4.28 Cu CU B:Cu500 4.19 Cu S1 B:Urs1002 2.26 Cu N1 B:Urs1002 2.69 Cu N2 B:Urs1002 4.05 Cu C7 B:Urs1002 2.77 Cu C4 B:Urs1002 4.05 Cu C3 B:Urs1002 3.57 Cu C2 B:Urs1002 4.59 interactive model: