Cadmium in the structure of Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus (pdb 1c6r)

The binding sites of Cadmium atom in the structure of Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus (pdb code 1c6r). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1c6r structure was solved by J.SCHNACKENBERG, M.E.THAN, K.MANN, G.WIEGAND, R.HUBER, W.REUTER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-1.9 Space group P21212 a (A) 35.560 b (A) 48.470 c (A) 43.920 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 26 Cadmium Binding Sites: Cadmium binding site 1 out of 4 in 1c6r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1c6r. 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: Asp3, A: Leu6, A: Hoh103, A: Hoh106, A: Hoh120, A: Hoh149, conact list: Atom Atom Distance (A) Cd CB A:Asp3 4.40 Cd OD2 A:Asp3 1.96 Cd OD1 A:Asp3 3.45 Cd CG A:Asp3 3.06 Cd CB A:Leu6 4.61 Cd CD2 A:Leu6 4.98 Cd O A:Hoh103 4.52 Cd O A:Hoh106 4.19 Cd O A:Hoh120 1.87 Cd O A:Hoh149 1.76 interactive model: Cadmium binding site 2 out of 4 in 1c6r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1c6r. 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: Asp69, A: Asp71, A: Glu72, A: Hoh103, A: Hoh136, A: Hoh143, A: Hoh151, conact list: Atom Atom Distance (A) Cd CB A:Asp69 4.27 Cd OD2 A:Asp69 1.99 Cd OD1 A:Asp69 2.94 Cd CG A:Asp69 2.83 Cd N A:Asp71 4.84 Cd CB A:Asp71 4.08 Cd OD2 A:Asp71 2.32 Cd OD1 A:Asp71 2.16 Cd CG A:Asp71 2.56 Cd CA A:Asp71 4.85 Cd N A:Glu72 4.77 Cd OE2 A:Glu72 4.38 Cd CD A:Glu72 4.49 Cd CG A:Glu72 4.31 Cd O A:Hoh103 4.78 Cd O A:Hoh136 4.39 Cd O A:Hoh143 4.58 Cd O A:Hoh151 2.66 interactive model: Cadmium binding site 3 out of 4 in 1c6r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 1c6r. 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: His30, A: Phe40, A: Hem90, A: Hoh134, A: Hoh148, conact list: Atom Atom Distance (A) Cd NE2 A:His30 2.67 Cd ND1 A:His30 4.74 Cd CD2 A:His30 3.26 Cd CE1 A:His30 3.81 Cd CG A:His30 4.52 Cd O A:Phe40 4.44 Cd CB A:Phe40 4.67 Cd CD1 A:Phe40 4.65 Cd O2D A:Hem90 4.11 Cd CGD A:Hem90 4.01 Cd O1D A:Hem90 3.13 Cd O A:Hoh134 4.84 Cd O A:Hoh148 1.56 interactive model: Cadmium binding site 4 out of 4 in 1c6r Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 1c6r. 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: Trp89, A: Hoh162, A: Hoh163, conact list: Atom Atom Distance (A) Cd N A:Trp89 4.95 Cd CB A:Trp89 4.74 Cd C A:Trp89 2.58 Cd CA A:Trp89 3.99 Cd O A:Trp89 1.64 Cd OXT A:Trp89 2.88 Cd O A:Hoh162 2.63 Cd O A:Hoh163 4.79 interactive model: