Cadmium in the structure of A More Complete Structure Of The The L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit (pdb 2qa4)

The binding sites of Cadmium atom in the structure of A More Complete Structure Of The The L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit (pdb code 2qa4). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2qa4 structure was solved by T.A.STEITZ, J.M.KAVRAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.0 Space group C2221 a (A) 214.490 b (A) 302.432 c (A) 578.056 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.1 Rfree (%) 28.8 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 2qa4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2qa4. 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: U: Cys6, U: Tyr8, U: Cys9, U: Gly10, U: Thr11, U: Cys32, U: Ser33, U: Cys36, conact list: Atom Atom Distance (A) Cd CB U:Cys6 3.59 Cd SG U:Cys6 2.98 Cd CB U:Tyr8 4.71 Cd CD2 U:Tyr8 4.80 Cd C U:Tyr8 4.89 Cd N U:Cys9 3.67 Cd CB U:Cys9 2.78 Cd SG U:Cys9 3.98 Cd C U:Cys9 4.66 Cd CA U:Cys9 3.80 Cd N U:Gly10 4.67 Cd OG1 U:Thr11 4.00 Cd N U:Cys32 4.34 Cd CB U:Cys32 4.17 Cd SG U:Cys32 3.04 Cd CA U:Cys32 4.81 Cd OG U:Ser33 4.76 Cd CB U:Cys36 3.79 Cd SG U:Cys36 2.69 interactive model: Cadmium binding site 2 out of 5 in 2qa4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2qa4. 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: Cys19, 1: Arg21, 1: Cys22, 1: Gly23, 1: Glu24, 1: Cys34, 1: Ser36, 1: Cys37, 1: Gly38, 1: Phe39, conact list: Atom Atom Distance (A) Cd O 1:Cys19 4.63 Cd CB 1:Cys19 2.75 Cd SG 1:Cys19 2.18 Cd C 1:Cys19 4.60 Cd CA 1:Cys19 4.22 Cd N 1:Arg21 4.85 Cd CB 1:Arg21 4.57 Cd CD 1:Arg21 4.98 Cd C 1:Arg21 4.51 Cd CA 1:Arg21 4.85 Cd N 1:Cys22 3.35 Cd CB 1:Cys22 3.09 Cd SG 1:Cys22 2.07 Cd C 1:Cys22 4.50 Cd CA 1:Cys22 3.75 Cd N 1:Gly23 4.41 Cd N 1:Glu24 4.77 Cd CB 1:Glu24 4.97 Cd CB 1:Cys34 3.41 Cd SG 1:Cys34 2.67 Cd CA 1:Cys34 4.87 Cd CB 1:Ser36 4.92 Cd N 1:Cys37 3.85 Cd CB 1:Cys37 3.13 Cd SG 1:Cys37 2.51 Cd C 1:Cys37 4.75 Cd CA 1:Cys37 4.05 Cd N 1:Gly38 4.87 Cd N 1:Phe39 4.96 Cd CB 1:Phe39 4.41 interactive model: Cadmium binding site 3 out of 5 in 2qa4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2qa4. 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: Z: Cys39, Z: Asn41, Z: Cys42, Z: Glu44, Z: Cys57, Z: Tyr59, Z: Cys60, Z: Tyr62, conact list: Atom Atom Distance (A) Cd CB Z:Cys39 3.87 Cd SG Z:Cys39 3.63 Cd CB Z:Asn41 4.32 Cd N Z:Cys42 4.20 Cd CB Z:Cys42 4.21 Cd SG Z:Cys42 3.09 Cd CA Z:Cys42 4.75 Cd N Z:Glu44 4.99 Cd CB Z:Glu44 4.79 Cd CB Z:Cys57 4.11 Cd SG Z:Cys57 3.90 Cd CB Z:Tyr59 4.77 Cd CD2 Z:Tyr59 4.21 Cd N Z:Cys60 4.16 Cd CB Z:Cys60 3.44 Cd SG Z:Cys60 4.61 Cd CA Z:Cys60 4.41 Cd CB Z:Tyr62 4.68 interactive model: Cadmium binding site 4 out of 5 in 2qa4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2qa4. 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: 3: Cys11, 3: His13, 3: Cys14, 3: Cys71, 3: Cys74, 3: Lys76, conact list: Atom Atom Distance (A) Cd CB 3:Cys11 4.08 Cd SG 3:Cys11 3.75 Cd CB 3:His13 3.94 Cd CD2 3:His13 4.77 Cd C 3:His13 4.73 Cd CG 3:His13 4.71 Cd CA 3:His13 4.77 Cd N 3:Cys14 3.89 Cd CB 3:Cys14 3.90 Cd CA 3:Cys14 4.53 Cd CB 3:Cys71 3.77 Cd SG 3:Cys71 4.25 Cd N 3:Cys74 4.61 Cd CB 3:Cys74 3.53 Cd SG 3:Cys74 4.56 Cd CA 3:Cys74 4.63 Cd O 3:Lys76 4.82 Cd N 3:Lys76 4.89 Cd CB 3:Lys76 4.71 interactive model: Cadmium binding site 5 out of 5 in 2qa4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2qa4. 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: O: Arg37, O: His40, conact list: Atom Atom Distance (A) Cd O O:Arg37 4.82 Cd CB O:Arg37 4.78 Cd CD O:Arg37 4.94 Cd CZ O:Arg37 4.78 Cd CG O:Arg37 4.29 Cd NE O:Arg37 4.53 Cd CB O:His40 3.86 Cd ND1 O:His40 3.04 Cd CE1 O:His40 4.04 Cd CG O:His40 3.85 interactive model: