Cadmium in the structure of Crystal Structure Of the Catalytic Core of An Rna Polymerase Ribozyme Complexed With An Antigen Binding Antibody Fragment (pdb 3ivk)

The binding sites of Cadmium atom in the structure of Crystal Structure Of the Catalytic Core of An Rna Polymerase Ribozyme Complexed With An Antigen Binding Antibody Fragment (pdb code 3ivk). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3ivk structure was solved by Y.KOLDOBSKAYA, E.M.DUGUID, D.M.SHECHNER, S.KOIDE, A.A.KOSSIAKOFF, D.P.BARTEL, J.A.PICCIRILLI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.1 Space group C2221 a (A) 207.499 b (A) 206.452 c (A) 135.926 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.7 Rfree (%) 22.5 Cadmium Binding Sites: Cadmium binding site 1 out of 2 in 3ivk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3ivk. 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: L: Ser1, L: Asp2, L: Pro96, H: Asp65, conact list: Atom Atom Distance (A) Cd OG L:Ser1 4.20 Cd CB L:Asp2 4.35 Cd OD2 L:Asp2 2.19 Cd OD1 L:Asp2 2.89 Cd CG L:Asp2 2.88 Cd CD L:Pro96 4.68 Cd CG L:Pro96 4.65 Cd CB H:Asp65 4.19 Cd OD2 H:Asp65 2.42 Cd OD1 H:Asp65 2.29 Cd CG H:Asp65 2.69 Cd CA H:Asp65 4.99 interactive model: Cadmium binding site 2 out of 2 in 3ivk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3ivk. 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: B: Ser1, B: Asp2, B: Pro96, A: Asp65, conact list: Atom Atom Distance (A) Cd OG B:Ser1 4.15 Cd CB B:Asp2 4.41 Cd OD2 B:Asp2 2.27 Cd OD1 B:Asp2 2.89 Cd CG B:Asp2 2.93 Cd CD B:Pro96 4.68 Cd CG B:Pro96 4.69 Cd CB A:Asp65 4.25 Cd OD2 A:Asp65 2.48 Cd OD1 A:Asp65 2.34 Cd CG A:Asp65 2.74 interactive model: