Cadmium in the structure of Chitosan Product Complex of Amycolatopsis Orientalis Exo- Chitosanase Csxa (pdb 2vzs)

The binding sites of Cadmium atom in the structure of Chitosan Product Complex of Amycolatopsis Orientalis Exo- Chitosanase Csxa (pdb code 2vzs). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2vzs structure was solved by A.LAMMERTS VAN BUEREN, M.G.GHINET, K.GREGG, A.FLEURY, R.BRZEZINSKI, A.B.BORASTON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.9 Space group P1211 a (A) 86.544 b (A) 121.810 c (A) 91.843 alpha (°) 90.00 beta (°) 90.42 gamma (°) 90.00 Rfactor (%) 17.3 Rfree (%) 22 Cadmium Binding Sites: Cadmium binding site 1 out of 6 in 2vzs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2vzs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asn299, A: His310, B: Ser62, B: Val65, B: Asp68, B: Lys187, B: Hoh2016, B: Hoh2026, B: Hoh2031, B: Hoh2188, B: Hoh2189, conact list: Atom Atom Distance (A) Cd CB A:Asn299 4.03 Cd ND2 A:Asn299 2.63 Cd OD1 A:Asn299 4.86 Cd CG A:Asn299 3.75 Cd NE2 A:His310 4.10 Cd ND1 A:His310 3.58 Cd CD2 A:His310 4.52 Cd CE1 A:His310 3.50 Cd CG A:His310 4.21 Cd O B:Ser62 4.22 Cd CB B:Ser62 3.79 Cd OG B:Ser62 4.12 Cd C B:Ser62 4.89 Cd CA B:Ser62 4.89 Cd O B:Val65 4.41 Cd OD2 B:Asp68 4.35 Cd OD1 B:Asp68 3.52 Cd CG B:Asp68 4.35 Cd CE B:Lys187 3.12 Cd CD B:Lys187 4.60 Cd NZ B:Lys187 2.51 Cd O B:Hoh2016 3.54 Cd O B:Hoh2026 4.80 Cd O B:Hoh2031 2.75 Cd O B:Hoh2188 4.56 Cd O B:Hoh2189 4.28 interactive model: Cadmium binding site 2 out of 6 in 2vzs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2vzs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Pro120, A: Tyr189, A: Hoh2081, A: Hoh2174, A: Hoh2175, conact list: Atom Atom Distance (A) Cd CD A:Pro120 3.86 Cd CG A:Pro120 3.91 Cd CD1 A:Tyr189 4.56 Cd CE1 A:Tyr189 4.22 Cd O A:Hoh2081 2.67 Cd O A:Hoh2174 2.72 Cd O A:Hoh2175 4.66 interactive model: Cadmium binding site 3 out of 6 in 2vzs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2vzs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gly425, A: Asn428, A: Gly429, A: Glu430, A: Glu431, A: Lys432, A: Gly433, A: Glu434, A: Pro435, A: Hoh2476, conact list: Atom Atom Distance (A) Cd O A:Gly425 3.54 Cd C A:Gly425 4.23 Cd CA A:Gly425 4.11 Cd O A:Asn428 4.71 Cd ND2 A:Asn428 2.69 Cd C A:Asn428 4.51 Cd OD1 A:Asn428 4.44 Cd CG A:Asn428 3.92 Cd O A:Gly429 2.89 Cd N A:Gly429 4.37 Cd C A:Gly429 4.01 Cd CA A:Gly429 4.68 Cd N A:Glu430 5.00 Cd C A:Glu430 4.90 Cd O A:Glu431 2.87 Cd N A:Glu431 4.66 Cd C A:Glu431 4.05 Cd CA A:Glu431 4.92 Cd O A:Lys432 4.40 Cd N A:Lys432 4.95 Cd C A:Lys432 4.29 Cd CA A:Lys432 4.98 Cd O A:Gly433 2.43 Cd N A:Gly433 4.22 Cd C A:Gly433 3.58 Cd CA A:Gly433 4.27 Cd N A:Glu434 4.61 Cd C A:Glu434 4.84 Cd CA A:Glu434 4.77 Cd N A:Pro435 4.84 Cd CD A:Pro435 4.67 Cd O A:Hoh2476 2.60 interactive model: Cadmium binding site 4 out of 6 in 2vzs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2vzs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His244, B: Ala245, B: Asp246, B: Leu292, B: Gly294, conact list: Atom Atom Distance (A) Cd NE2 B:His244 2.29 Cd ND1 B:His244 4.40 Cd CD2 B:His244 3.14 Cd CE1 B:His244 3.35 Cd CG B:His244 4.34 Cd O B:Ala245 4.59 Cd CB B:Asp246 4.29 Cd OD2 B:Asp246 2.74 Cd OD1 B:Asp246 2.28 Cd CG B:Asp246 2.83 Cd CA B:Asp246 4.82 Cd CD2 B:Leu292 4.96 Cd CA B:Gly294 4.30 interactive model: Cadmium binding site 5 out of 6 in 2vzs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2vzs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His244, B: Asp296, B: Hoh2279, B: Hoh2319, conact list: Atom Atom Distance (A) Cd ND1 B:His244 4.15 Cd CE1 B:His244 3.94 Cd CB B:Asp296 4.24 Cd OD2 B:Asp296 2.32 Cd OD1 B:Asp296 2.49 Cd CG B:Asp296 2.73 Cd O B:Hoh2279 4.44 Cd O B:Hoh2319 2.51 interactive model: Cadmium binding site 6 out of 6 in 2vzs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2vzs. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Gly425, B: Asn428, B: Gly429, B: Glu430, B: Glu431, B: Lys432, B: Gly433, B: Glu434, conact list: Atom Atom Distance (A) Cd O B:Gly425 4.00 Cd C B:Gly425 4.66 Cd CA B:Gly425 4.44 Cd O B:Asn428 4.59 Cd CB B:Asn428 4.93 Cd ND2 B:Asn428 4.33 Cd C B:Asn428 4.42 Cd OD1 B:Asn428 2.66 Cd CG B:Asn428 3.76 Cd CA B:Asn428 4.98 Cd O B:Gly429 2.70 Cd N B:Gly429 4.33 Cd C B:Gly429 3.81 Cd CA B:Gly429 4.67 Cd N B:Glu430 4.64 Cd C B:Glu430 4.43 Cd CA B:Glu430 4.66 Cd O B:Glu431 2.50 Cd N B:Glu431 4.16 Cd C B:Glu431 3.65 Cd CA B:Glu431 4.49 Cd O B:Lys432 4.18 Cd N B:Lys432 4.56 Cd C B:Lys432 4.03 Cd CA B:Lys432 4.60 Cd O B:Gly433 2.52 Cd N B:Gly433 4.03 Cd C B:Gly433 3.65 Cd CA B:Gly433 4.25 Cd N B:Glu434 4.74 interactive model: