Cadmium in the structure of Crystal Structure of Rh(Nbd)/Apo-Fr (pdb 2zur)

The binding sites of Cadmium atom in the structure of Crystal Structure of Rh(Nbd)/Apo-Fr (pdb code 2zur). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2zur structure was solved by S.ABE, K.HIRATA, T.UENO, N.SHIMIZU, M.YAMAMOTO, M.TAKATA, Y.WATANABE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 37.0-1.8 Space group F432 a (A) 181.276 b (A) 181.276 c (A) 181.276 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 19.6 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 2zur Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2zur. 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: X: Asp80, X: Hoh213, X: Hoh217, conact list: Atom Atom Distance (A) Cd CB X:Asp80 4.26 Cd OD2 X:Asp80 2.41 Cd OD1 X:Asp80 2.38 Cd CG X:Asp80 2.75 Cd O X:Hoh213 4.38 Cd O X:Hoh217 4.58 interactive model: Cadmium binding site 2 out of 5 in 2zur Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2zur. 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: X: Glu56, X: Glu57, X: Glu60, X: Hoh369, X: Hoh381, conact list: Atom Atom Distance (A) Cd OE2 X:Glu56 4.92 Cd CD X:Glu56 4.85 Cd CG X:Glu56 4.99 Cd CG X:Glu57 4.46 Cd OE1 X:Glu60 2.37 Cd OE2 X:Glu60 3.15 Cd CD X:Glu60 3.11 Cd CG X:Glu60 4.58 Cd O X:Hoh369 3.11 Cd O X:Hoh381 1.97 interactive model: Cadmium binding site 3 out of 5 in 2zur Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2zur. 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: X: Ser9, X: Thr10, X: Glu11, X: Gln120, X: Hoh236, conact list: Atom Atom Distance (A) Cd CB X:Ser9 4.56 Cd N X:Thr10 4.75 Cd OG1 X:Thr10 3.88 Cd OE1 X:Glu11 2.74 Cd OE2 X:Glu11 2.49 Cd CD X:Glu11 2.98 Cd CG X:Glu11 4.52 Cd NE2 X:Gln120 4.80 Cd OE1 X:Gln120 4.79 Cd O X:Hoh236 3.05 interactive model: Cadmium binding site 4 out of 5 in 2zur Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2zur. 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: X: Asp127, X: Glu130, X: Ser131, X: Cd179, conact list: Atom Atom Distance (A) Cd OD1 X:Asp127 3.51 Cd CG X:Asp127 4.70 Cd CB X:Glu130 4.84 Cd OG X:Ser131 4.50 Cd CD X:Cd179 4.66 interactive model: Cadmium binding site 5 out of 5 in 2zur Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2zur. 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: X: Cys126, X: Asp127, X: Glu130, X: Cd178, X: Rh183, X: Hoh192, conact list: Atom Atom Distance (A) Cd O X:Cys126 4.74 Cd C X:Cys126 4.66 Cd CB X:Cys126 4.76 Cd N X:Asp127 4.47 Cd CB X:Asp127 4.88 Cd CA X:Asp127 4.44 Cd CB X:Glu130 4.81 Cd CD X:Cd178 4.66 Cd RH1 X:Rh183 3.19 Cd O X:Hoh192 4.14 interactive model: