Cadmium in the structure of Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit (pdb 3g4s)

The binding sites of Cadmium atom in the structure of Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit (pdb code 3g4s). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3g4s structure was solved by G.GUREL, G.BLAHA, P.B.MOORE, T.A.STEITZ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 49.8-3.2 Space group C2221 a (A) 212.270 b (A) 299.840 c (A) 574.137 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.5 Rfree (%) 29 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 3g4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3g4s. 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: Leu7, O: Arg37, O: His40, O: Hoh3002, O: Hoh5322, O: Hoh5650, conact list: Atom Atom Distance (A) Cd CD1 O:Leu7 4.88 Cd CD2 O:Leu7 4.96 Cd CZ O:Arg37 4.53 Cd CG O:Arg37 4.91 Cd NE O:Arg37 4.78 Cd NH2 O:Arg37 4.60 Cd NH1 O:Arg37 4.82 Cd NE2 O:His40 4.52 Cd CB O:His40 4.19 Cd ND1 O:His40 2.59 Cd CD2 O:His40 4.77 Cd CE1 O:His40 3.29 Cd CG O:His40 3.75 Cd O O:Hoh3002 4.00 Cd O O:Hoh5322 3.83 Cd O O:Hoh5650 3.24 interactive model: Cadmium binding site 2 out of 5 in 3g4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3g4s. 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: Phe31, U: Cys32, U: Ser33, U: Cys36, conact list: Atom Atom Distance (A) Cd CB U:Cys6 3.97 Cd SG U:Cys6 3.09 Cd CB U:Tyr8 4.80 Cd CD2 U:Tyr8 4.90 Cd N U:Cys9 3.84 Cd CB U:Cys9 2.93 Cd SG U:Cys9 3.98 Cd C U:Cys9 4.84 Cd CA U:Cys9 3.98 Cd N U:Gly10 4.92 Cd N U:Thr11 4.99 Cd CB U:Thr11 4.44 Cd OG1 U:Thr11 3.03 Cd C U:Phe31 4.64 Cd CA U:Phe31 4.77 Cd N U:Cys32 3.56 Cd CB U:Cys32 3.51 Cd SG U:Cys32 3.24 Cd C U:Cys32 4.92 Cd CA U:Cys32 4.09 Cd N U:Ser33 4.67 Cd CB U:Cys36 3.74 Cd SG U:Cys36 3.08 interactive model: Cadmium binding site 3 out of 5 in 3g4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3g4s. 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: Asp85, Z: Tyr86, conact list: Atom Atom Distance (A) Cd SG Z:Cys63 4.30 Cd O Z:Asn65 4.28 Cd CB Z:Asn65 3.76 Cd ND2 Z:Asn65 4.08 Cd C Z:Asn65 4.36 Cd CG Z:Asn65 4.48 Cd CA Z:Asn65 4.64 Cd N Z:Cys66 4.83 Cd CB Z:Cys66 4.43 Cd SG Z:Cys66 3.90 Cd CB Z:Cys81 4.60 Cd SG Z:Cys81 3.90 Cd CB Z:Tyr83 3.89 Cd CE2 Z:Tyr83 4.27 Cd CD2 Z:Tyr83 3.30 Cd C Z:Tyr83 4.35 Cd CG Z:Tyr83 4.07 Cd CA Z:Tyr83 4.66 Cd O Z:Cys84 4.06 Cd N Z:Cys84 3.19 Cd CB Z:Cys84 3.07 Cd SG Z:Cys84 4.16 Cd C Z:Cys84 3.73 Cd CA Z:Cys84 3.51 Cd N Z:Asp85 4.17 Cd N Z:Tyr86 4.29 Cd CB Z:Tyr86 4.07 Cd CA Z:Tyr86 4.80 interactive model: Cadmium binding site 4 out of 5 in 3g4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3g4s. 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 CB 1:Cys19 3.08 Cd SG 1:Cys19 2.69 Cd CA 1:Cys19 4.59 Cd CB 1:Arg21 4.72 Cd C 1:Arg21 4.83 Cd N 1:Cys22 3.72 Cd CB 1:Cys22 3.44 Cd SG 1:Cys22 2.65 Cd C 1:Cys22 4.78 Cd CA 1:Cys22 4.10 Cd N 1:Gly23 4.46 Cd O 1:Glu24 4.95 Cd N 1:Glu24 4.99 Cd CB 1:Cys34 3.51 Cd SG 1:Cys34 2.57 Cd CA 1:Cys34 4.91 Cd CB 1:Ser36 4.81 Cd C 1:Ser36 4.96 Cd N 1:Cys37 3.85 Cd CB 1:Cys37 3.31 Cd SG 1:Cys37 2.54 Cd C 1:Cys37 4.84 Cd CA 1:Cys37 4.13 Cd N 1:Gly38 4.89 Cd CB 1:Phe39 4.56 interactive model: Cadmium binding site 5 out of 5 in 3g4s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3g4s. 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: Thr9, 3: Tyr10, 3: Cys11, 3: Cys14, 3: Glu16, 3: His17, 3: Gln18, 3: His20, 3: Cys71, conact list: Atom Atom Distance (A) Cd O 3:Thr9 3.98 Cd O 3:Tyr10 4.73 Cd C 3:Tyr10 4.30 Cd CA 3:Tyr10 4.82 Cd O 3:Cys11 4.55 Cd N 3:Cys11 3.91 Cd CB 3:Cys11 3.10 Cd SG 3:Cys11 4.07 Cd C 3:Cys11 4.84 Cd CA 3:Cys11 4.10 Cd CB 3:Cys14 3.51 Cd SG 3:Cys14 3.66 Cd CA 3:Cys14 4.93 Cd O 3:Glu16 3.48 Cd N 3:Glu16 4.81 Cd C 3:Glu16 4.08 Cd CG 3:Glu16 4.95 Cd CA 3:Glu16 4.95 Cd N 3:His17 4.59 Cd C 3:His17 4.53 Cd CA 3:His17 4.57 Cd O 3:Gln18 4.65 Cd N 3:Gln18 3.72 Cd OE1 3:Gln18 3.79 Cd CB 3:Gln18 3.79 Cd CD 3:Gln18 4.22 Cd C 3:Gln18 4.84 Cd CG 3:Gln18 4.56 Cd CA 3:Gln18 4.28 Cd NE2 3:His20 3.77 Cd ND1 3:His20 4.42 Cd CE1 3:His20 3.29 Cd CB 3:Cys71 4.37 Cd SG 3:Cys71 4.18 interactive model: