Cadmium in the structure of Crystal Structure Of Cca-Phe-Cap-Biotin Bound Simultaneously At Half Occupancy to Both The A-Site and P- Site of The the 50S Ribosomal Subunit. (pdb 1q86)

The binding sites of Cadmium atom in the structure of Crystal Structure Of Cca-Phe-Cap-Biotin Bound Simultaneously At Half Occupancy to Both The A-Site and P- Site of The the 50S Ribosomal Subunit. (pdb code 1q86). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1q86 structure was solved by J.L.HANSEN, M.T.SCHMEING, 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) 213.163 b (A) 301.288 c (A) 575.397 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.4 Rfree (%) 26.4 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 1q86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1q86. 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: Arg37, P: His40, A: Hoh5532, A: Hoh5772, P: Hoh3002, conact list: Atom Atom Distance (A) Cd CB P:Arg37 4.92 Cd CZ P:Arg37 4.99 Cd CG P:Arg37 4.69 Cd NE P:Arg37 4.95 Cd CA P:Arg37 4.95 Cd NE2 P:His40 4.62 Cd CB P:His40 3.79 Cd ND1 P:His40 2.57 Cd CD2 P:His40 4.67 Cd CE1 P:His40 3.48 Cd CG P:His40 3.55 Cd O A:Hoh5532 3.55 Cd O A:Hoh5772 2.88 Cd O P:Hoh3002 4.72 interactive model: Cadmium binding site 2 out of 5 in 1q86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1q86. 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: Ser33, V: Cys36, conact list: Atom Atom Distance (A) Cd CB V:Cys6 3.13 Cd SG V:Cys6 2.44 Cd CA V:Cys6 4.63 Cd CB V:Tyr8 4.51 Cd C V:Tyr8 4.89 Cd N V:Cys9 3.78 Cd CB V:Cys9 3.42 Cd SG V:Cys9 2.55 Cd C V:Cys9 4.97 Cd CA V:Cys9 4.19 Cd N V:Gly10 4.80 Cd OG1 V:Thr11 4.32 Cd N V:Cys32 4.00 Cd CB V:Cys32 3.63 Cd SG V:Cys32 2.32 Cd C V:Cys32 4.93 Cd CA V:Cys32 4.38 Cd N V:Ser33 4.60 Cd OG V:Ser33 4.44 Cd CB V:Cys36 3.69 Cd SG V:Cys36 2.34 interactive model: Cadmium binding site 3 out of 5 in 1q86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1q86. 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 3.19 Cd SG 1:Cys39 2.33 Cd CA 1:Cys39 4.65 Cd CB 1:Val41 4.59 Cd C 1:Val41 4.86 Cd CG1 1:Val41 4.69 Cd N 1:Cys42 3.73 Cd CB 1:Cys42 3.45 Cd SG 1:Cys42 2.91 Cd C 1:Cys42 4.79 Cd CA 1:Cys42 4.16 Cd CB 1:Cys57 3.26 Cd SG 1:Cys57 2.45 Cd CA 1:Cys57 4.76 Cd CB 1:His59 4.52 Cd CD2 1:His59 4.69 Cd N 1:Cys60 3.90 Cd CB 1:Cys60 3.49 Cd SG 1:Cys60 2.23 Cd CA 1:Cys60 4.27 Cd CB 1:Tyr62 4.73 interactive model: Cadmium binding site 4 out of 5 in 1q86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1q86. 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: Glu24, 2: Cys34, 2: Ser36, 2: Cys37, 2: Phe39, 2: Hoh8420, conact list: Atom Atom Distance (A) Cd CB 2:Cys19 3.07 Cd SG 2:Cys19 2.58 Cd CA 2:Cys19 4.56 Cd CB 2:Arg21 4.62 Cd CD 2:Arg21 4.89 Cd C 2:Arg21 4.65 Cd CA 2:Arg21 4.99 Cd N 2:Cys22 3.57 Cd CB 2:Cys22 3.19 Cd SG 2:Cys22 2.36 Cd C 2:Cys22 4.64 Cd CA 2:Cys22 3.93 Cd N 2:Gly23 4.74 Cd O 2:Glu24 4.89 Cd N 2:Glu24 4.92 Cd CB 2:Cys34 3.26 Cd SG 2:Cys34 2.42 Cd CA 2:Cys34 4.71 Cd CB 2:Ser36 4.70 Cd C 2:Ser36 4.91 Cd N 2:Cys37 3.80 Cd CB 2:Cys37 3.29 Cd SG 2:Cys37 2.36 Cd C 2:Cys37 4.86 Cd CA 2:Cys37 4.12 Cd N 2:Phe39 4.96 Cd CB 2:Phe39 4.32 Cd O 2:Hoh8420 4.72 interactive model: Cadmium binding site 5 out of 5 in 1q86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 1q86. 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: His13, 4: Cys14, 4: Gln18, 4: Cys71, 4: Cys74, 4: Hoh8535, 4: Hoh8558, conact list: Atom Atom Distance (A) Cd CB 4:Cys11 3.51 Cd SG 4:Cys11 2.43 Cd CA 4:Cys11 4.92 Cd CB 4:His13 4.48 Cd C 4:His13 4.69 Cd N 4:Cys14 3.54 Cd CB 4:Cys14 3.08 Cd SG 4:Cys14 2.35 Cd CA 4:Cys14 3.84 Cd OE1 4:Gln18 4.78 Cd CB 4:Cys71 3.07 Cd SG 4:Cys71 2.22 Cd CA 4:Cys71 4.52 Cd N 4:Cys74 4.11 Cd CB 4:Cys74 3.45 Cd SG 4:Cys74 2.34 Cd CA 4:Cys74 4.36 Cd O 4:Hoh8535 4.54 Cd O 4:Hoh8558 2.97 interactive model: