Cadmium in the structure of Co-Crystal Structure Of Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb 1k9m)

The binding sites of Cadmium atom in the structure of Co-Crystal Structure Of Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1k9m). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1k9m structure was solved by J.L.HANSEN, J.A.IPPOLITO, N.BAN, P.NISSEN, P.B.MOORE, T.A.STEITZ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.0 Space group C2221 a (A) 212.902 b (A) 300.474 c (A) 575.176 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.9 Rfree (%) 26.2 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 1k9m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1k9m. 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: P: Leu7, P: Arg37, P: His40, A: Hoh4330, P: Hoh5322, P: Hoh5650, conact list: Atom Atom Distance (A) Cd CD2 P:Leu7 4.96 Cd O P:Arg37 4.81 Cd CB P:Arg37 4.48 Cd CD P:Arg37 4.53 Cd CZ P:Arg37 4.20 Cd CG P:Arg37 3.80 Cd NE P:Arg37 4.30 Cd NH2 P:Arg37 4.65 Cd NH1 P:Arg37 4.27 Cd CA P:Arg37 4.61 Cd NE2 P:His40 4.77 Cd CB P:His40 4.15 Cd ND1 P:His40 2.86 Cd CD2 P:His40 4.89 Cd CE1 P:His40 3.65 Cd CG P:His40 3.84 Cd O A:Hoh4330 4.36 Cd O P:Hoh5322 3.25 Cd O P:Hoh5650 2.69 interactive model: Cadmium binding site 2 out of 5 in 1k9m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1k9m. 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: V: Cys6, V: Tyr8, V: Cys9, V: Gly10, V: Thr11, V: Cys32, V: Cys36, conact list: Atom Atom Distance (A) Cd O V:Cys6 4.95 Cd CB V:Cys6 3.43 Cd SG V:Cys6 3.11 Cd CA V:Cys6 4.84 Cd N V:Tyr8 4.56 Cd CB V:Tyr8 3.76 Cd CD2 V:Tyr8 4.20 Cd C V:Tyr8 4.06 Cd CG V:Tyr8 4.48 Cd CA V:Tyr8 4.32 Cd N V:Cys9 2.98 Cd CB V:Cys9 2.95 Cd SG V:Cys9 3.35 Cd C V:Cys9 4.45 Cd CA V:Cys9 3.52 Cd N V:Gly10 4.44 Cd OG1 V:Thr11 4.85 Cd N V:Cys32 4.63 Cd CB V:Cys32 4.60 Cd SG V:Cys32 4.07 Cd CB V:Cys36 3.32 Cd SG V:Cys36 3.08 Cd CA V:Cys36 4.78 interactive model: Cadmium binding site 3 out of 5 in 1k9m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1k9m. 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: 1: Cys39, 1: Val41, 1: Cys42, 1: Cys57, 1: His59, 1: Cys60, 1: Tyr62, conact list: Atom Atom Distance (A) Cd CB 1:Cys39 3.71 Cd SG 1:Cys39 3.24 Cd CB 1:Val41 4.30 Cd C 1:Val41 4.67 Cd CG1 1:Val41 4.34 Cd CA 1:Val41 4.95 Cd N 1:Cys42 3.56 Cd CB 1:Cys42 3.31 Cd SG 1:Cys42 3.59 Cd C 1:Cys42 4.74 Cd CA 1:Cys42 4.02 Cd CB 1:Cys57 3.80 Cd SG 1:Cys57 3.72 Cd CB 1:His59 4.85 Cd CD2 1:His59 4.58 Cd N 1:Cys60 4.05 Cd CB 1:Cys60 3.32 Cd SG 1:Cys60 3.37 Cd CA 1:Cys60 4.27 Cd CB 1:Tyr62 4.57 interactive model: Cadmium binding site 4 out of 5 in 1k9m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1k9m. 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: 2: Cys19, 2: Arg21, 2: Cys22, 2: Gly23, 2: Cys34, 2: Ser36, 2: Cys37, 2: Gly38, 2: Phe39, 2: Hoh1020, conact list: Atom Atom Distance (A) Cd CB 2:Cys19 3.04 Cd SG 2:Cys19 2.54 Cd CA 2:Cys19 4.52 Cd CB 2:Arg21 4.59 Cd C 2:Arg21 4.71 Cd CA 2:Arg21 4.99 Cd N 2:Cys22 3.66 Cd CB 2:Cys22 3.41 Cd SG 2:Cys22 2.67 Cd C 2:Cys22 4.82 Cd CA 2:Cys22 4.09 Cd N 2:Gly23 4.89 Cd CB 2:Cys34 3.17 Cd SG 2:Cys34 2.57 Cd CA 2:Cys34 4.63 Cd CB 2:Ser36 4.91 Cd C 2:Ser36 4.93 Cd N 2:Cys37 3.83 Cd CB 2:Cys37 3.30 Cd SG 2:Cys37 2.31 Cd C 2:Cys37 4.84 Cd CA 2:Cys37 4.12 Cd N 2:Gly38 4.87 Cd N 2:Phe39 4.85 Cd CB 2:Phe39 4.27 Cd O 2:Hoh1020 4.82 interactive model: Cadmium binding site 5 out of 5 in 1k9m Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1k9m. 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: 4: Cys11, 4: Cys14, 4: Gln18, 4: Cys71, 4: Cys74, 4: Hoh8563, conact list: Atom Atom Distance (A) Cd CB 4:Cys11 3.73 Cd SG 4:Cys11 3.49 Cd N 4:Cys14 3.77 Cd CB 4:Cys14 2.87 Cd SG 4:Cys14 3.67 Cd CA 4:Cys14 3.88 Cd NE2 4:Gln18 4.43 Cd OE1 4:Gln18 3.94 Cd CB 4:Gln18 4.88 Cd CD 4:Gln18 4.27 Cd CB 4:Cys71 3.49 Cd SG 4:Cys71 3.07 Cd CA 4:Cys71 4.96 Cd N 4:Cys74 4.07 Cd CB 4:Cys74 3.57 Cd SG 4:Cys74 4.01 Cd CA 4:Cys74 4.46 Cd O 4:Hoh8563 2.98 interactive model: