Copper in the structure of Laccase From Streptomyces Coelicolor (pdb 3cg8)

The binding sites of Copper atom in the structure of Laccase From Streptomyces Coelicolor (pdb code 3cg8). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 3cg8 structure was solved by T.SKALOVA, J.DOHNALEK, L.H.OSTERGAARD, P.R.OSTERGAARD, P.KOLENKO, J.DUSKOVA, J.HASEK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.5-2.7 Space group P43212 a (A) 180.868 b (A) 180.868 c (A) 177.111 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.2 Rfree (%) 19.4 Copper Binding Sites: Copper binding site 1 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 3cg8. 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: Tyr230, A: His231, A: Thr232, A: Cys288, A: Val290, A: His293, A: Met298, conact list: Atom Atom Distance (A) Cu O A:Tyr230 4.03 Cu C A:Tyr230 4.76 Cu NE2 A:His231 4.11 Cu N A:His231 4.65 Cu CB A:His231 3.33 Cu ND1 A:His231 2.01 Cu CD2 A:His231 4.14 Cu C A:His231 4.73 Cu CE1 A:His231 3.00 Cu CG A:His231 3.01 Cu CA A:His231 3.68 Cu N A:Thr232 4.62 Cu CB A:Cys288 3.26 Cu SG A:Cys288 2.20 Cu CA A:Cys288 4.65 Cu CB A:Val290 4.13 Cu CG2 A:Val290 4.11 Cu CG1 A:Val290 4.98 Cu NE2 A:His293 3.98 Cu CB A:His293 3.30 Cu ND1 A:His293 1.89 Cu CD2 A:His293 4.03 Cu CE1 A:His293 2.86 Cu CG A:His293 2.92 Cu CA A:His293 4.80 Cu CE A:Met298 3.91 Cu CG A:Met298 4.96 Cu SD A:Met298 3.45 interactive model: Copper binding site 2 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 3cg8. 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: His234, A: His289, C: His102, C: His104, C: His154, C: His156, C: His226, C: Ala266, A: Cu413, A: Cu414, A: O501, C: Hoh681, conact list: Atom Atom Distance (A) Cu NE2 A:His234 4.22 Cu CD2 A:His234 4.36 Cu CE1 A:His234 4.90 Cu NE2 A:His289 1.97 Cu ND1 A:His289 4.00 Cu CD2 A:His289 2.95 Cu CE1 A:His289 2.91 Cu CG A:His289 4.04 Cu NE2 C:His102 4.21 Cu CD2 C:His102 3.86 Cu NE2 C:His104 1.94 Cu ND1 C:His104 3.99 Cu CD2 C:His104 3.03 Cu CE1 C:His104 2.83 Cu CG C:His104 4.11 Cu NE2 C:His154 4.87 Cu CE1 C:His154 4.25 Cu NE2 C:His156 2.06 Cu ND1 C:His156 4.14 Cu CD2 C:His156 3.04 Cu CE1 C:His156 3.04 Cu CG C:His156 4.18 Cu CE1 C:His226 4.97 Cu CB C:Ala266 4.01 Cu CU A:Cu413 4.96 Cu CU A:Cu414 3.86 Cu O A:O501 2.44 Cu O C:Hoh681 4.69 interactive model: Copper binding site 3 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 3cg8. 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: His234, A: His236, A: Met285, A: His287, A: His289, C: His102, C: His158, C: His164, A: Cu412, A: Cu414, A: O501, C: Hoh681, conact list: Atom Atom Distance (A) Cu NE2 A:His234 4.30 Cu CD2 A:His234 3.96 Cu NE2 A:His236 2.06 Cu ND1 A:His236 4.06 Cu CD2 A:His236 3.19 Cu CE1 A:His236 2.88 Cu CG A:His236 4.24 Cu SD A:Met285 4.66 Cu NE2 A:His287 2.33 Cu ND1 A:His287 4.37 Cu CD2 A:His287 3.29 Cu CE1 A:His287 3.26 Cu CG A:His287 4.42 Cu NE2 A:His289 4.70 Cu NE2 C:His102 4.03 Cu CD2 C:His102 4.36 Cu CE1 C:His102 4.63 Cu NE2 C:His158 2.35 Cu ND1 C:His158 4.43 Cu CD2 C:His158 3.33 Cu CE1 C:His158 3.30 Cu CG C:His158 4.48 Cu ND1 C:His164 4.75 Cu CU A:Cu412 4.96 Cu CU A:Cu414 3.63 Cu O A:O501 2.54 Cu O C:Hoh681 3.59 interactive model: Copper binding site 4 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 3cg8. 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: His234, A: His236, A: His287, A: His289, C: His102, C: Val103, C: His104, C: Tyr108, A: Cu412, A: Cu413, A: O501, C: Hoh613, conact list: Atom Atom Distance (A) Cu NE2 A:His234 1.92 Cu ND1 A:His234 4.02 Cu CD2 A:His234 2.89 Cu CE1 A:His234 2.93 Cu CG A:His234 4.03 Cu NE2 A:His236 3.22 Cu N A:His236 4.84 Cu CB A:His236 4.73 Cu ND1 A:His236 4.35 Cu CD2 A:His236 3.07 Cu CE1 A:His236 4.03 Cu CG A:His236 3.85 Cu CA A:His236 4.57 Cu NE2 A:His287 4.96 Cu NE2 A:His289 4.81 Cu NE2 C:His102 1.79 Cu ND1 C:His102 3.83 Cu CD2 C:His102 2.89 Cu CE1 C:His102 2.69 Cu CG C:His102 3.95 Cu O C:Val103 4.69 Cu NE2 C:His104 3.70 Cu ND1 C:His104 4.46 Cu CD2 C:His104 4.04 Cu CE1 C:His104 4.00 Cu CG C:His104 4.49 Cu OH C:Tyr108 4.59 Cu CU A:Cu412 3.86 Cu CU A:Cu413 3.63 Cu O A:O501 2.64 Cu O C:Hoh613 2.82 interactive model: Copper binding site 5 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 3cg8. 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: Phe195, B: Tyr230, B: His231, B: Thr232, B: Cys288, B: Val290, B: His293, B: Met298, conact list: Atom Atom Distance (A) Cu CD2 B:Phe195 5.00 Cu O B:Tyr230 4.12 Cu C B:Tyr230 4.83 Cu NE2 B:His231 4.04 Cu N B:His231 4.69 Cu CB B:His231 3.37 Cu ND1 B:His231 1.97 Cu CD2 B:His231 4.11 Cu C B:His231 4.70 Cu CE1 B:His231 2.91 Cu CG B:His231 3.02 Cu CA B:His231 3.69 Cu N B:Thr232 4.54 Cu CB B:Cys288 3.23 Cu SG B:Cys288 2.19 Cu CA B:Cys288 4.65 Cu CB B:Val290 4.16 Cu CG2 B:Val290 4.12 Cu CG1 B:Val290 4.99 Cu NE2 B:His293 4.08 Cu CB B:His293 3.27 Cu ND1 B:His293 1.97 Cu CD2 B:His293 4.09 Cu CE1 B:His293 2.97 Cu CG B:His293 2.96 Cu CA B:His293 4.79 Cu CE B:Met298 4.12 Cu CG B:Met298 4.90 Cu SD B:Met298 3.43 interactive model: Copper binding site 6 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 3cg8. 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: His102, A: His104, A: His154, A: His156, A: His226, A: Ala266, B: His234, B: His289, B: Cu413, B: Cu414, B: O501, A: Hoh708, conact list: Atom Atom Distance (A) Cu NE2 A:His102 4.17 Cu CD2 A:His102 3.87 Cu NE2 A:His104 1.92 Cu ND1 A:His104 4.01 Cu CD2 A:His104 2.95 Cu CE1 A:His104 2.88 Cu CG A:His104 4.07 Cu NE2 A:His154 4.83 Cu CE1 A:His154 4.16 Cu NE2 A:His156 2.02 Cu ND1 A:His156 4.07 Cu CD2 A:His156 3.05 Cu CE1 A:His156 2.94 Cu CG A:His156 4.15 Cu CE1 A:His226 4.87 Cu CB A:Ala266 3.95 Cu NE2 B:His234 4.20 Cu CD2 B:His234 4.34 Cu CE1 B:His234 4.91 Cu NE2 B:His289 2.03 Cu ND1 B:His289 4.05 Cu CD2 B:His289 2.95 Cu CE1 B:His289 3.00 Cu CG B:His289 4.06 Cu CU B:Cu413 4.97 Cu CU B:Cu414 3.91 Cu O B:O501 2.35 Cu O A:Hoh708 4.73 interactive model: Copper binding site 7 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Copper in the PDB 3cg8. 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: His102, A: His158, A: His164, B: His234, B: His236, B: Met285, B: His287, B: His289, B: Cu412, B: Cu414, B: O501, A: Hoh708, conact list: Atom Atom Distance (A) Cu NE2 A:His102 4.06 Cu CD2 A:His102 4.44 Cu CE1 A:His102 4.60 Cu NE2 A:His158 2.27 Cu ND1 A:His158 4.38 Cu CD2 A:His158 3.18 Cu CE1 A:His158 3.29 Cu CG A:His158 4.36 Cu CD2 A:His164 4.54 Cu NE2 B:His234 4.24 Cu CD2 B:His234 3.95 Cu NE2 B:His236 2.12 Cu ND1 B:His236 4.10 Cu CD2 B:His236 3.27 Cu CE1 B:His236 2.89 Cu CG B:His236 4.30 Cu SD B:Met285 4.66 Cu NE2 B:His287 2.41 Cu ND1 B:His287 4.46 Cu CD2 B:His287 3.36 Cu CE1 B:His287 3.35 Cu CG B:His287 4.50 Cu NE2 B:His289 4.71 Cu CD2 B:His289 4.96 Cu CU B:Cu412 4.97 Cu CU B:Cu414 3.98 Cu O B:O501 2.70 Cu O A:Hoh708 3.78 interactive model: Copper binding site 8 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Copper in the PDB 3cg8. 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: His102, A: Val103, A: His104, A: Tyr108, B: His234, B: His236, B: Cu412, B: Cu413, B: O501, A: Hoh612, A: Hoh738, conact list: Atom Atom Distance (A) Cu NE2 A:His102 1.79 Cu ND1 A:His102 3.81 Cu CD2 A:His102 2.95 Cu CE1 A:His102 2.63 Cu CG A:His102 3.97 Cu O A:Val103 4.26 Cu C A:Val103 4.87 Cu NE2 A:His104 3.52 Cu ND1 A:His104 4.26 Cu CD2 A:His104 3.78 Cu CE1 A:His104 3.86 Cu CG A:His104 4.22 Cu CA A:His104 4.91 Cu OH A:Tyr108 4.51 Cu NE2 B:His234 1.90 Cu ND1 B:His234 3.90 Cu CD2 B:His234 3.04 Cu CE1 B:His234 2.73 Cu CG B:His234 4.08 Cu NE2 B:His236 3.48 Cu N B:His236 4.91 Cu CB B:His236 4.88 Cu ND1 B:His236 4.44 Cu CD2 B:His236 3.42 Cu CE1 B:His236 4.13 Cu CG B:His236 4.04 Cu CA B:His236 4.63 Cu CU B:Cu412 3.91 Cu CU B:Cu413 3.98 Cu O B:O501 2.62 Cu O A:Hoh612 2.83 Cu O A:Hoh738 4.87 interactive model: Copper binding site 9 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Copper in the PDB 3cg8. 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: Phe195, C: Tyr230, C: His231, C: Thr232, C: Cys288, C: Val290, C: His293, C: Met298, conact list: Atom Atom Distance (A) Cu CD2 C:Phe195 4.95 Cu O C:Tyr230 4.09 Cu C C:Tyr230 4.78 Cu NE2 C:His231 4.11 Cu N C:His231 4.67 Cu CB C:His231 3.32 Cu ND1 C:His231 2.01 Cu CD2 C:His231 4.13 Cu C C:His231 4.75 Cu CE1 C:His231 3.00 Cu CG C:His231 3.00 Cu CA C:His231 3.68 Cu N C:Thr232 4.63 Cu CB C:Cys288 3.18 Cu SG C:Cys288 2.16 Cu CA C:Cys288 4.59 Cu CB C:Val290 4.13 Cu CG2 C:Val290 4.12 Cu CG1 C:Val290 4.92 Cu NE2 C:His293 4.02 Cu CB C:His293 3.24 Cu ND1 C:His293 1.91 Cu CD2 C:His293 4.03 Cu CE1 C:His293 2.92 Cu CG C:His293 2.90 Cu CA C:His293 4.77 Cu CE C:Met298 4.14 Cu CG C:Met298 4.88 Cu SD C:Met298 3.40 interactive model: Copper binding site 10 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Copper in the PDB 3cg8. 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: His102, B: His104, B: His154, B: His156, B: His226, B: Ala266, C: His234, C: His289, C: Cu414, C: O501, B: Hoh702, conact list: Atom Atom Distance (A) Cu NE2 B:His102 4.43 Cu CD2 B:His102 3.94 Cu NE2 B:His104 1.93 Cu ND1 B:His104 3.98 Cu CD2 B:His104 3.01 Cu CE1 B:His104 2.83 Cu CG B:His104 4.09 Cu NE2 B:His154 4.87 Cu CE1 B:His154 4.21 Cu NE2 B:His156 2.14 Cu ND1 B:His156 4.20 Cu CD2 B:His156 3.13 Cu CE1 B:His156 3.09 Cu CG B:His156 4.24 Cu CE1 B:His226 4.97 Cu CB B:Ala266 4.02 Cu NE2 C:His234 4.26 Cu CD2 C:His234 4.36 Cu CE1 C:His234 4.95 Cu NE2 C:His289 2.10 Cu ND1 C:His289 4.14 Cu CD2 C:His289 3.03 Cu CE1 C:His289 3.07 Cu CG C:His289 4.15 Cu CU C:Cu414 3.28 Cu O C:O501 2.74 Cu O B:Hoh702 4.55 interactive model: Copper binding site 11 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Copper in the PDB 3cg8. 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: His102, B: His158, B: His164, C: His234, C: His236, C: Met285, C: His287, C: His289, C: Cu414, C: O501, B: Hoh702, conact list: Atom Atom Distance (A) Cu NE2 B:His102 4.16 Cu CD2 B:His102 4.47 Cu CE1 B:His102 4.71 Cu NE2 B:His158 2.22 Cu ND1 B:His158 4.33 Cu CD2 B:His158 3.16 Cu CE1 B:His158 3.23 Cu CG B:His158 4.33 Cu ND1 B:His164 4.60 Cu NE2 C:His234 4.33 Cu CD2 C:His234 3.98 Cu NE2 C:His236 2.11 Cu ND1 C:His236 4.10 Cu CD2 C:His236 3.26 Cu CE1 C:His236 2.90 Cu CG C:His236 4.29 Cu SD C:Met285 4.55 Cu NE2 C:His287 2.37 Cu ND1 C:His287 4.38 Cu CD2 C:His287 3.29 Cu CE1 C:His287 3.29 Cu CG C:His287 4.41 Cu NE2 C:His289 4.81 Cu CU C:Cu414 3.64 Cu O C:O501 2.37 Cu O B:Hoh702 3.53 interactive model: Copper binding site 12 out of 12 in 3cg8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Copper in the PDB 3cg8. 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: His102, B: Val103, B: His104, B: His156, B: His158, C: His234, C: His236, C: His287, C: His289, C: Cu412, C: Cu413, C: O501, B: Hoh613, conact list: Atom Atom Distance (A) Cu NE2 B:His102 1.94 Cu ND1 B:His102 4.07 Cu CD2 B:His102 2.62 Cu CE1 B:His102 3.13 Cu CG B:His102 3.87 Cu O B:Val103 4.86 Cu NE2 B:His104 3.23 Cu ND1 B:His104 4.18 Cu CD2 B:His104 3.64 Cu CE1 B:His104 3.64 Cu CG B:His104 4.22 Cu NE2 B:His156 4.51 Cu NE2 B:His158 4.94 Cu CD2 B:His158 4.85 Cu NE2 C:His234 2.03 Cu ND1 C:His234 4.06 Cu CD2 C:His234 2.87 Cu CE1 C:His234 3.05 Cu CG C:His234 4.01 Cu NE2 C:His236 3.55 Cu ND1 C:His236 4.74 Cu CD2 C:His236 3.69 Cu CE1 C:His236 4.25 Cu CG C:His236 4.46 Cu NE2 C:His287 4.86 Cu NE2 C:His289 4.37 Cu CD2 C:His289 4.62 Cu CU C:Cu412 3.28 Cu CU C:Cu413 3.64 Cu O C:O501 2.72 Cu O B:Hoh613 2.84 interactive model: