Cadmium in the structure of Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis (pdb 1oyr)

The binding sites of Cadmium atom in the structure of Crystal Structure of the Phosphorolytic Exoribonuclease Rnase pH From Bacillus Subtilis (pdb code 1oyr). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1oyr structure was solved by L.S.HARLOW, A.KADZIOLA, K.F.JENSEN, S.LARSEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.9-3.1 Space group P212121 a (A) 99.790 b (A) 146.490 c (A) 152.250 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 27.8 Rfree (%) 28.8 Cadmium Binding Sites: Cadmium binding site 1 out of 3 in 1oyr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1oyr. 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: A: His3, A: Glu179, conact list: Atom Atom Distance (A) Cd NE2 A:His3 4.33 Cd CB A:His3 4.12 Cd ND1 A:His3 2.38 Cd CD2 A:His3 4.53 Cd CE1 A:His3 3.09 Cd CG A:His3 3.56 Cd OE1 A:Glu179 2.53 Cd OE2 A:Glu179 2.60 Cd CD A:Glu179 2.80 Cd CG A:Glu179 4.18 interactive model: Cadmium binding site 2 out of 3 in 1oyr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1oyr. 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: E: His3, E: Ser183, conact list: Atom Atom Distance (A) Cd NE2 E:His3 3.24 Cd ND1 E:His3 3.81 Cd CD2 E:His3 4.56 Cd CE1 E:His3 2.67 Cd CG E:His3 4.81 Cd OG E:Ser183 4.52 interactive model: Cadmium binding site 3 out of 3 in 1oyr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1oyr. 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: D: His3, D: Glu179, conact list: Atom Atom Distance (A) Cd NE2 D:His3 3.07 Cd CB D:His3 4.09 Cd ND1 D:His3 3.62 Cd CD2 D:His3 2.90 Cd CE1 D:His3 3.49 Cd CG D:His3 3.29 Cd OE1 D:Glu179 2.43 Cd CB D:Glu179 4.95 Cd OE2 D:Glu179 2.33 Cd CD D:Glu179 2.53 Cd CG D:Glu179 3.82 interactive model: