Cadmium in the structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A (pdb 3ccv)

The binding sites of Cadmium atom in the structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2616A (pdb code 3ccv). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3ccv structure was solved by G.BLAHA, G.GUREL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.9 Space group C2221 a (A) 211.752 b (A) 299.012 c (A) 574.480 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 22.5 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 3ccv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3ccv. 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, 0: Hoh4360, 0: Hoh6040, 0: Hoh6276, conact list: Atom Atom Distance (A) Cd CB O:Arg37 4.87 Cd CZ O:Arg37 4.73 Cd CG O:Arg37 4.52 Cd NE O:Arg37 4.77 Cd NE2 O:His40 4.59 Cd CB O:His40 3.86 Cd ND1 O:His40 2.56 Cd CD2 O:His40 4.68 Cd CE1 O:His40 3.43 Cd CG O:His40 3.58 Cd O 0:Hoh4360 4.28 Cd O 0:Hoh6040 3.42 Cd O 0:Hoh6276 2.84 interactive model: Cadmium binding site 2 out of 5 in 3ccv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3ccv. 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 3.23 Cd SG U:Cys6 2.44 Cd CA U:Cys6 4.72 Cd CB U:Tyr8 4.60 Cd C U:Tyr8 4.86 Cd N U:Cys9 3.69 Cd CB U:Cys9 3.23 Cd SG U:Cys9 2.31 Cd C U:Cys9 4.86 Cd CA U:Cys9 4.03 Cd N U:Gly10 4.74 Cd OG1 U:Thr11 4.40 Cd N U:Cys32 3.89 Cd CB U:Cys32 3.44 Cd SG U:Cys32 2.45 Cd C U:Cys32 4.78 Cd CA U:Cys32 4.21 Cd N U:Ser33 4.62 Cd OG U:Ser33 4.58 Cd CB U:Cys36 3.54 Cd SG U:Cys36 2.44 Cd CA U:Cys36 4.95 interactive model: Cadmium binding site 3 out of 5 in 3ccv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3ccv. 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: Cys63, Z: Asn65, Z: Cys66, Z: Cys81, Z: Tyr83, Z: Cys84, Z: Tyr86, conact list: Atom Atom Distance (A) Cd CB Z:Cys63 3.39 Cd SG Z:Cys63 2.36 Cd CA Z:Cys63 4.79 Cd N Z:Asn65 4.67 Cd CB Z:Asn65 3.58 Cd ND2 Z:Asn65 4.46 Cd C Z:Asn65 4.45 Cd CG Z:Asn65 4.59 Cd CA Z:Asn65 4.47 Cd N Z:Cys66 3.49 Cd CB Z:Cys66 3.59 Cd SG Z:Cys66 2.88 Cd C Z:Cys66 4.96 Cd CA Z:Cys66 4.15 Cd CB Z:Cys81 3.22 Cd SG Z:Cys81 2.51 Cd CA Z:Cys81 4.72 Cd CB Z:Tyr83 4.36 Cd CD2 Z:Tyr83 4.29 Cd C Z:Tyr83 4.88 Cd CG Z:Tyr83 4.84 Cd N Z:Cys84 3.77 Cd CB Z:Cys84 3.39 Cd SG Z:Cys84 2.31 Cd C Z:Cys84 4.84 Cd CA Z:Cys84 4.14 Cd CB Z:Tyr86 4.64 interactive model: Cadmium binding site 4 out of 5 in 3ccv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3ccv. 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: Cys34, 1: Ser36, 1: Cys37, 1: Gly38, 1: Phe39, 1: Hoh8968, conact list: Atom Atom Distance (A) Cd CB 1:Cys19 3.07 Cd SG 1:Cys19 2.52 Cd CA 1:Cys19 4.56 Cd N 1:Arg21 5.00 Cd CB 1:Arg21 4.65 Cd CD 1:Arg21 4.92 Cd C 1:Arg21 4.68 Cd CA 1:Arg21 4.98 Cd N 1:Cys22 3.57 Cd CB 1:Cys22 3.08 Cd SG 1:Cys22 2.37 Cd C 1:Cys22 4.67 Cd CA 1:Cys22 3.89 Cd N 1:Gly23 4.71 Cd CB 1:Cys34 3.19 Cd SG 1:Cys34 2.37 Cd CA 1:Cys34 4.63 Cd CB 1:Ser36 4.88 Cd C 1:Ser36 4.97 Cd N 1:Cys37 3.81 Cd CB 1:Cys37 3.32 Cd SG 1:Cys37 2.39 Cd C 1:Cys37 4.78 Cd CA 1:Cys37 4.10 Cd N 1:Gly38 4.86 Cd N 1:Phe39 4.73 Cd CB 1:Phe39 4.09 Cd O 1:Hoh8968 4.98 interactive model: Cadmium binding site 5 out of 5 in 3ccv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3ccv. 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: Gln18, 3: Cys71, 3: Cys74, 3: Hoh8963, 3: Hoh8985, conact list: Atom Atom Distance (A) Cd CB 3:Cys11 3.56 Cd SG 3:Cys11 2.40 Cd CA 3:Cys11 4.93 Cd CB 3:His13 4.48 Cd C 3:His13 4.79 Cd N 3:Cys14 3.78 Cd CB 3:Cys14 3.40 Cd SG 3:Cys14 2.44 Cd CA 3:Cys14 4.17 Cd NE2 3:Gln18 4.91 Cd CB 3:Gln18 4.86 Cd CG 3:Gln18 4.27 Cd CB 3:Cys71 3.09 Cd SG 3:Cys71 2.34 Cd CA 3:Cys71 4.55 Cd N 3:Cys74 4.08 Cd CB 3:Cys74 3.65 Cd SG 3:Cys74 2.37 Cd CA 3:Cys74 4.41 Cd O 3:Hoh8963 4.56 Cd O 3:Hoh8985 4.83 interactive model: