Cadmium in the structure of Horse Spleen Apoferritin (pdb 2w0o)

The binding sites of Cadmium atom in the structure of Horse Spleen Apoferritin (pdb code 2w0o). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2w0o structure was solved by N.DE VAL, J.P.DECLERCQ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 104.8-1.5 Space group F432 a (A) 182.000 b (A) 182.000 c (A) 182.000 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 23.6 Cadmium Binding Sites: Cadmium binding site 1 out of 7 in 2w0o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2w0o. 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: Asp80, conact list: Atom Atom Distance (A) Cd CB A:Asp80 4.38 Cd OD2 A:Asp80 2.54 Cd OD1 A:Asp80 2.42 Cd CG A:Asp80 2.84 interactive model: Cadmium binding site 2 out of 7 in 2w0o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2w0o. 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: Glu130, A: Hoh2186, A: Hoh2187, conact list: Atom Atom Distance (A) Cd OE1 A:Glu130 2.49 Cd OE2 A:Glu130 3.58 Cd CD A:Glu130 3.39 Cd CG A:Glu130 4.76 Cd O A:Hoh2186 4.21 Cd O A:Hoh2187 4.23 interactive model: Cadmium binding site 3 out of 7 in 2w0o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2w0o. 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: Glu56, A: Glu57, A: Glu60, A: Cd1177, A: Hoh2099, A: Hoh2107, conact list: Atom Atom Distance (A) Cd OE1 A:Glu56 4.56 Cd CB A:Glu56 4.95 Cd OE2 A:Glu56 2.44 Cd CD A:Glu56 3.44 Cd CG A:Glu56 3.75 Cd OE1 A:Glu57 4.25 Cd OE2 A:Glu57 2.84 Cd CD A:Glu57 3.92 Cd OE1 A:Glu60 2.63 Cd OE2 A:Glu60 2.30 Cd CD A:Glu60 2.81 Cd CG A:Glu60 4.30 Cd CD A:Cd1177 4.99 Cd O A:Hoh2099 4.01 Cd O A:Hoh2107 4.56 interactive model: Cadmium binding site 4 out of 7 in 2w0o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2w0o. 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: Ser9, A: Thr10, A: Glu11, A: Gln120, A: Hoh2012, A: Hoh2027, A: Hoh2032, A: Hoh2180, conact list: Atom Atom Distance (A) Cd CB A:Ser9 4.52 Cd N A:Thr10 4.73 Cd OG1 A:Thr10 3.90 Cd N A:Glu11 4.96 Cd OE1 A:Glu11 2.38 Cd OE2 A:Glu11 2.58 Cd CD A:Glu11 2.85 Cd CG A:Glu11 4.40 Cd NE2 A:Gln120 4.76 Cd OE1 A:Gln120 4.57 Cd O A:Hoh2012 3.93 Cd O A:Hoh2027 2.88 Cd O A:Hoh2032 4.18 Cd O A:Hoh2180 2.56 interactive model: Cadmium binding site 5 out of 7 in 2w0o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2w0o. 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: Glu53, A: Glu56, A: Cd1175, A: Hoh2099, conact list: Atom Atom Distance (A) Cd OE1 A:Glu53 2.97 Cd OE2 A:Glu53 3.25 Cd CD A:Glu53 3.50 Cd OE1 A:Glu56 2.53 Cd OE2 A:Glu56 3.05 Cd CD A:Glu56 3.13 Cd CG A:Glu56 4.58 Cd CD A:Cd1175 4.99 Cd O A:Hoh2099 4.13 interactive model: Cadmium binding site 6 out of 7 in 2w0o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2w0o. 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: conact list: Atom Atom Distance (A) interactive model: Cadmium binding site 7 out of 7 in 2w0o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 2w0o. 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: Lys142, A: Asp146, A: Hoh2196, A: Hoh2197, conact list: Atom Atom Distance (A) Cd NZ A:Lys142 4.05 Cd OD2 A:Asp146 4.76 Cd O A:Hoh2196 4.35 Cd O A:Hoh2197 4.74 interactive model: