Copper in the structure of Crystal Structure of MET150GLY Afnir With Methylsulfanyl Methane Bound (pdb 1zdq)

The binding sites of Copper atom in the structure of Crystal Structure of MET150GLY Afnir With Methylsulfanyl Methane Bound (pdb code 1zdq). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1zdq structure was solved by H.J.WIJMA, I.S.MACPHERSON, M.ALEXANDRE, R.E.M.DIEDERIX, G.W.CANTERS, M.E.P.MURPHY, M.P.VERBEET, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 84.5-1.8 Space group P212121 a (A) 61.968 b (A) 103.012 c (A) 146.903 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.6 Rfree (%) 19.9 Copper Binding Sites: Copper binding site 1 out of 6 in 1zdq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1zdq. 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: Met62, A: Met94, A: His95, A: Asn96, A: Cys136, A: Pro138, A: His145, A: Msm1507, conact list: Atom Atom Distance (A) Cu CB A:Met62 4.19 Cu CE A:Met62 3.19 Cu CG A:Met62 3.44 Cu SD A:Met62 2.32 Cu O A:Met94 4.35 Cu NE2 A:His95 4.16 Cu N A:His95 4.96 Cu CB A:His95 3.54 Cu ND1 A:His95 2.12 Cu CD2 A:His95 4.26 Cu C A:His95 4.96 Cu CE1 A:His95 3.02 Cu CG A:His95 3.17 Cu CA A:His95 3.96 Cu N A:Asn96 4.77 Cu CB A:Cys136 3.28 Cu SG A:Cys136 2.26 Cu CA A:Cys136 4.71 Cu CD A:Pro138 4.70 Cu CG A:Pro138 4.34 Cu NE2 A:His145 4.05 Cu CB A:His145 3.53 Cu ND1 A:His145 2.00 Cu CD2 A:His145 4.17 Cu CE1 A:His145 2.89 Cu CG A:His145 3.10 Cu CA A:His145 4.65 Cu SG1 A:Msm1507 4.45 interactive model: Copper binding site 2 out of 6 in 1zdq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1zdq. 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: Asp98, A: His100, A: His135, B: His255, B: His306, B: Leu308, A: Hoh1669, A: Hoh1746, A: Hoh1876, B: Hoh1838, conact list: Atom Atom Distance (A) Cu OD2 A:Asp98 4.54 Cu OD1 A:Asp98 3.66 Cu CG A:Asp98 4.29 Cu NE2 A:His100 2.02 Cu ND1 A:His100 4.08 Cu CD2 A:His100 3.09 Cu CE1 A:His100 2.92 Cu CG A:His100 4.19 Cu NE2 A:His135 2.11 Cu ND1 A:His135 4.22 Cu CD2 A:His135 3.05 Cu CE1 A:His135 3.12 Cu CG A:His135 4.22 Cu NE2 B:His255 3.82 Cu CD2 B:His255 4.08 Cu CE1 B:His255 4.47 Cu CG B:His255 4.83 Cu NE2 B:His306 2.04 Cu ND1 B:His306 4.10 Cu CD2 B:His306 3.08 Cu CE1 B:His306 2.97 Cu CG B:His306 4.19 Cu CD2 B:Leu308 4.95 Cu O A:Hoh1669 4.19 Cu O A:Hoh1746 4.83 Cu O A:Hoh1876 1.96 Cu O B:Hoh1838 2.17 interactive model: Copper binding site 3 out of 6 in 1zdq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1zdq. 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: Met62, B: Met94, B: His95, B: Asn96, B: Cys136, B: Pro138, B: His145, B: Msm1508, conact list: Atom Atom Distance (A) Cu CB B:Met62 4.25 Cu CE B:Met62 3.19 Cu CG B:Met62 3.50 Cu SD B:Met62 2.44 Cu O B:Met94 4.35 Cu NE2 B:His95 4.19 Cu N B:His95 4.96 Cu CB B:His95 3.47 Cu ND1 B:His95 2.12 Cu CD2 B:His95 4.25 Cu C B:His95 4.98 Cu CE1 B:His95 3.07 Cu CG B:His95 3.13 Cu CA B:His95 3.97 Cu N B:Asn96 4.79 Cu CB B:Cys136 3.25 Cu SG B:Cys136 2.16 Cu CA B:Cys136 4.66 Cu CD B:Pro138 4.72 Cu CG B:Pro138 4.28 Cu NE2 B:His145 4.07 Cu CB B:His145 3.53 Cu ND1 B:His145 2.06 Cu CD2 B:His145 4.17 Cu CE1 B:His145 2.93 Cu CG B:His145 3.11 Cu CA B:His145 4.67 Cu SG1 B:Msm1508 4.58 interactive model: Copper binding site 4 out of 6 in 1zdq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1zdq. 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: Asp98, B: His100, B: His135, C: His255, C: His306, C: Leu308, B: Hoh1656, B: Hoh1718, B: Hoh1839, C: Hoh1818, conact list: Atom Atom Distance (A) Cu CB B:Asp98 4.95 Cu OD2 B:Asp98 4.49 Cu OD1 B:Asp98 3.62 Cu CG B:Asp98 4.17 Cu NE2 B:His100 2.06 Cu ND1 B:His100 4.12 Cu CD2 B:His100 3.10 Cu CE1 B:His100 2.98 Cu CG B:His100 4.21 Cu NE2 B:His135 2.04 Cu ND1 B:His135 4.15 Cu CD2 B:His135 3.01 Cu CE1 B:His135 3.05 Cu CG B:His135 4.17 Cu NE2 C:His255 4.07 Cu ND1 C:His255 4.66 Cu CD2 C:His255 4.61 Cu CE1 C:His255 4.12 Cu CG C:His255 4.96 Cu NE2 C:His306 2.13 Cu ND1 C:His306 4.19 Cu CD2 C:His306 3.17 Cu CE1 C:His306 3.05 Cu CG C:His306 4.28 Cu CD2 C:Leu308 4.86 Cu O B:Hoh1656 4.13 Cu O B:Hoh1718 4.80 Cu O B:Hoh1839 2.04 Cu O C:Hoh1818 2.31 interactive model: Copper binding site 5 out of 6 in 1zdq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 1zdq. 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: Met62, C: Met94, C: His95, C: Asn96, C: Cys136, C: Pro138, C: His145, C: Msm1509, conact list: Atom Atom Distance (A) Cu CB C:Met62 4.29 Cu CE C:Met62 3.23 Cu CG C:Met62 3.43 Cu SD C:Met62 2.42 Cu O C:Met94 4.31 Cu NE2 C:His95 4.24 Cu N C:His95 4.90 Cu CB C:His95 3.42 Cu ND1 C:His95 2.16 Cu CD2 C:His95 4.26 Cu C C:His95 4.96 Cu CE1 C:His95 3.14 Cu CG C:His95 3.13 Cu CA C:His95 3.93 Cu N C:Asn96 4.81 Cu CB C:Cys136 3.27 Cu SG C:Cys136 2.22 Cu CA C:Cys136 4.70 Cu CD C:Pro138 4.72 Cu CG C:Pro138 4.33 Cu NE2 C:His145 4.16 Cu CB C:His145 3.49 Cu ND1 C:His145 2.15 Cu CD2 C:His145 4.21 Cu CE1 C:His145 3.06 Cu CG C:His145 3.13 Cu CA C:His145 4.65 Cu SG1 C:Msm1509 4.51 interactive model: Copper binding site 6 out of 6 in 1zdq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 1zdq. 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: His255, A: Ile257, A: His306, A: Leu308, C: Asp98, C: His100, C: His135, A: Hoh1548, A: Hoh1877, C: Hoh1655, conact list: Atom Atom Distance (A) Cu NE2 A:His255 4.05 Cu ND1 A:His255 4.28 Cu CD2 A:His255 4.75 Cu CE1 A:His255 3.73 Cu CG A:His255 4.90 Cu CG1 A:Ile257 4.79 Cu NE2 A:His306 2.09 Cu ND1 A:His306 4.16 Cu CD2 A:His306 3.14 Cu CE1 A:His306 3.01 Cu CG A:His306 4.25 Cu CD2 A:Leu308 4.99 Cu OD2 C:Asp98 4.74 Cu OD1 C:Asp98 3.46 Cu CG C:Asp98 4.33 Cu NE2 C:His100 2.04 Cu ND1 C:His100 4.07 Cu CD2 C:His100 3.13 Cu CE1 C:His100 2.91 Cu CG C:His100 4.21 Cu NE2 C:His135 2.13 Cu ND1 C:His135 4.26 Cu CD2 C:His135 3.02 Cu CE1 C:His135 3.20 Cu CG C:His135 4.21 Cu O A:Hoh1548 4.83 Cu O A:Hoh1877 2.31 Cu O C:Hoh1655 3.96 interactive model: