Cadmium in the structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb 2eik)

The binding sites of Cadmium atom in the structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 2eik). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2eik structure was solved by K.MURAMOTO, K.HIRATA, K.SHINZAWA-ITOH, S.YOKO-O, E.YAMASHITA, H.AOYAMA, T.TSUKIHARA, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.1 Space group P212121 a (A) 183.321 b (A) 206.525 c (A) 178.159 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 22.8 Cadmium Binding Sites: Cadmium binding site 1 out of 6 in 2eik Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2eik. 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: Tyr502, A: His503, C: Met10, L: His2, A: Hoh2077, A: Hoh2078, A: Hoh2079, A: Hoh2084, L: Hoh2089, conact list: Atom Atom Distance (A) Cd CD1 A:Tyr502 4.91 Cd CE1 A:Tyr502 4.70 Cd NE2 A:His503 2.22 Cd ND1 A:His503 4.10 Cd CD2 A:His503 3.32 Cd CE1 A:His503 2.91 Cd CG A:His503 4.31 Cd CB C:Met10 4.99 Cd NE2 L:His2 2.22 Cd ND1 L:His2 4.13 Cd CD2 L:His2 3.35 Cd CE1 L:His2 2.93 Cd CG L:His2 4.35 Cd O A:Hoh2077 2.40 Cd O A:Hoh2078 2.38 Cd O A:Hoh2079 4.77 Cd O A:Hoh2084 4.97 Cd O L:Hoh2089 4.22 interactive model: Cadmium binding site 2 out of 6 in 2eik Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2eik. 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: C: His148, C: Met152, C: His232, C: Glu236, C: Hoh2027, C: Hoh2230, C: Hoh2409, conact list: Atom Atom Distance (A) Cd NE2 C:His148 2.26 Cd ND1 C:His148 4.19 Cd CD2 C:His148 3.42 Cd CE1 C:His148 2.97 Cd CG C:His148 4.42 Cd CE C:Met152 3.99 Cd CG C:Met152 3.57 Cd SD C:Met152 2.61 Cd NE2 C:His232 2.23 Cd ND1 C:His232 4.30 Cd CD2 C:His232 3.31 Cd CE1 C:His232 3.10 Cd CG C:His232 4.41 Cd OE1 C:Glu236 2.37 Cd OE2 C:Glu236 3.92 Cd CD C:Glu236 3.17 Cd CG C:Glu236 3.83 Cd O C:Hoh2027 2.30 Cd O C:Hoh2230 4.87 Cd O C:Hoh2409 2.30 interactive model: Cadmium binding site 3 out of 6 in 2eik Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2eik. 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: His78, E: Lys79, E: Glu80, E: Hoh4904, I: Hoh4355, conact list: Atom Atom Distance (A) Cd NE2 E:His78 4.34 Cd N E:His78 4.95 Cd CB E:His78 3.77 Cd ND1 E:His78 2.28 Cd CD2 E:His78 4.47 Cd C E:His78 4.76 Cd CE1 E:His78 3.13 Cd CG E:His78 3.37 Cd CA E:His78 3.90 Cd N E:Lys79 4.97 Cd OE1 E:Glu80 2.52 Cd OE2 E:Glu80 2.53 Cd CD E:Glu80 2.65 Cd CG E:Glu80 3.92 Cd O E:Hoh4904 2.44 Cd O I:Hoh4355 4.02 interactive model: Cadmium binding site 4 out of 6 in 2eik Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2eik. 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: N: Tyr502, N: His503, Y: His2, N: Hoh3077, N: Hoh3078, N: Hoh3079, N: Hoh3084, Y: Hoh3089, conact list: Atom Atom Distance (A) Cd CD1 N:Tyr502 4.96 Cd CE1 N:Tyr502 4.65 Cd NE2 N:His503 2.26 Cd ND1 N:His503 4.25 Cd CD2 N:His503 3.41 Cd CE1 N:His503 3.05 Cd CG N:His503 4.45 Cd NE2 Y:His2 2.27 Cd ND1 Y:His2 4.20 Cd CD2 Y:His2 3.41 Cd CE1 Y:His2 3.01 Cd CG Y:His2 4.42 Cd O N:Hoh3077 2.39 Cd O N:Hoh3078 2.37 Cd O N:Hoh3079 4.98 Cd O N:Hoh3084 4.97 Cd O Y:Hoh3089 4.39 interactive model: Cadmium binding site 5 out of 6 in 2eik Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2eik. 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: P: His148, P: Met152, P: His232, P: Glu236, P: Hoh3027, P: Hoh3230, P: Hoh3409, conact list: Atom Atom Distance (A) Cd NE2 P:His148 2.26 Cd ND1 P:His148 4.22 Cd CD2 P:His148 3.43 Cd CE1 P:His148 2.99 Cd CG P:His148 4.45 Cd CE P:Met152 3.82 Cd CG P:Met152 3.59 Cd SD P:Met152 2.50 Cd NE2 P:His232 2.27 Cd ND1 P:His232 4.34 Cd CD2 P:His232 3.35 Cd CE1 P:His232 3.14 Cd CG P:His232 4.46 Cd OE1 P:Glu236 2.30 Cd OE2 P:Glu236 3.82 Cd CD P:Glu236 3.09 Cd CG P:Glu236 3.86 Cd O P:Hoh3027 2.32 Cd O P:Hoh3230 4.85 Cd O P:Hoh3409 2.34 interactive model: Cadmium binding site 6 out of 6 in 2eik Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2eik. 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: N: Glu506, P: His3, N: Hoh3084, conact list: Atom Atom Distance (A) Cd OE1 N:Glu506 3.95 Cd OE2 N:Glu506 2.35 Cd CD N:Glu506 3.48 Cd CG N:Glu506 4.75 Cd NE2 P:His3 4.22 Cd CB P:His3 3.77 Cd ND1 P:His3 2.18 Cd CD2 P:His3 4.39 Cd CE1 P:His3 3.00 Cd CG P:His3 3.32 Cd O N:Hoh3084 4.33 interactive model: