Cadmium in the structure of Cytochrome C6 (pdb 1cyj)

The binding sites of Cadmium atom in the structure of Cytochrome C6 (pdb code 1cyj). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1cyj structure was solved by C.A.KERFELD, T.O.YEATES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.9 Space group I23 a (A) 81.600 b (A) 81.600 c (A) 81.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.7 Rfree (%) n/a Cadmium Binding Sites: Cadmium binding site 1 out of 4 in 1cyj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1cyj. 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: Arg66, A: Leu67, A: Ser68, A: Glu71, conact list: Atom Atom Distance (A) Cd O A:Arg66 4.45 Cd CD2 A:Leu67 4.94 Cd CA A:Leu67 4.73 Cd N A:Ser68 4.45 Cd CB A:Ser68 4.84 Cd OG A:Ser68 4.65 Cd OE1 A:Glu71 2.46 Cd OE2 A:Glu71 2.41 Cd CD A:Glu71 2.74 Cd CG A:Glu71 4.20 interactive model: Cadmium binding site 2 out of 4 in 1cyj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1cyj. 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: Asp2, A: Ala4, A: Leu5, A: Hoh424, A: Hoh463, conact list: Atom Atom Distance (A) Cd CB A:Asp2 4.38 Cd OD2 A:Asp2 2.26 Cd OD1 A:Asp2 2.86 Cd CG A:Asp2 2.91 Cd CB A:Ala4 4.40 Cd N A:Leu5 4.49 Cd CB A:Leu5 4.58 Cd O A:Hoh424 2.06 Cd O A:Hoh463 4.34 interactive model: Cadmium binding site 3 out of 4 in 1cyj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1cyj. 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: Ile50, A: Glu54, A: Glu69, A: Gln73, A: Hoh403, A: Hoh405, A: Hoh419, A: Hoh449, conact list: Atom Atom Distance (A) Cd CG2 A:Ile50 4.96 Cd OE1 A:Glu54 2.86 Cd OE2 A:Glu54 2.66 Cd CD A:Glu54 3.11 Cd CG A:Glu54 4.59 Cd OE1 A:Glu69 3.01 Cd OE2 A:Glu69 2.62 Cd CD A:Glu69 3.16 Cd CG A:Glu69 4.62 Cd NE2 A:Gln73 5.00 Cd O A:Hoh403 1.89 Cd O A:Hoh405 4.55 Cd O A:Hoh419 1.93 Cd O A:Hoh449 4.50 interactive model: Cadmium binding site 4 out of 4 in 1cyj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1cyj. 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: Glu47, A: Hoh422, A: Hoh456, A: Hoh469, conact list: Atom Atom Distance (A) Cd OE1 A:Glu47 3.15 Cd OE2 A:Glu47 4.60 Cd CD A:Glu47 4.09 Cd O A:Hoh422 1.79 Cd O A:Hoh456 2.84 Cd O A:Hoh469 3.41 interactive model: