Cadmium in the structure of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized With Haemin in Basic Conditions (pdb 2v2o)

The binding sites of Cadmium atom in the structure of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized With Haemin in Basic Conditions (pdb code 2v2o). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2v2o 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) 106.0-1.9 Space group F432 a (A) 183.801 b (A) 183.801 c (A) 183.801 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 23.6 Cadmium Binding Sites: Cadmium binding site 1 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2v2o. 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: Asp127, A: Glu130, A: Ser131, conact list: Atom Atom Distance (A) Cd OD1 A:Asp127 3.56 Cd CG A:Asp127 4.64 Cd OE1 A:Glu130 4.34 Cd OG A:Ser131 4.63 interactive model: Cadmium binding site 2 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2v2o. 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: Cd1173, conact list: Atom Atom Distance (A) Cd CD A:Cd1173 3.95 interactive model: Cadmium binding site 3 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2v2o. 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, A: Hoh2088, A: Hoh2090, conact list: Atom Atom Distance (A) Cd CB A:Asp80 4.40 Cd OD2 A:Asp80 2.13 Cd OD1 A:Asp80 3.13 Cd CG A:Asp80 3.00 Cd O A:Hoh2088 4.43 Cd O A:Hoh2090 4.67 interactive model: Cadmium binding site 4 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2v2o. 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: Cys126, A: Asp127, A: Glu130, A: Cd1171, conact list: Atom Atom Distance (A) Cd O A:Cys126 4.85 Cd CB A:Cys126 4.37 Cd C A:Cys126 4.57 Cd N A:Asp127 4.47 Cd CA A:Asp127 4.73 Cd OE1 A:Glu130 3.12 Cd OE2 A:Glu130 3.48 Cd CD A:Glu130 3.66 Cd CD A:Cd1171 3.95 interactive model: Cadmium binding site 5 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2v2o. 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: Asp38, A: Glu45, A: Cys48, conact list: Atom Atom Distance (A) Cd CB A:Asp38 4.04 Cd OD2 A:Asp38 4.87 Cd OD1 A:Asp38 3.10 Cd CG A:Asp38 3.86 Cd CA A:Asp38 4.48 Cd O A:Glu45 4.67 Cd CB A:Glu45 4.86 Cd OE2 A:Glu45 4.74 Cd CD A:Glu45 4.90 Cd CG A:Glu45 4.06 Cd CA A:Glu45 4.65 Cd CB A:Cys48 3.48 Cd SG A:Cys48 2.80 Cd CA A:Cys48 4.92 interactive model: Cadmium binding site 6 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2v2o. 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: Glu57, A: Glu60, A: Glu136, conact list: Atom Atom Distance (A) Cd OE1 A:Glu57 2.51 Cd OE2 A:Glu57 3.15 Cd CD A:Glu57 3.17 Cd CG A:Glu57 4.62 Cd OE1 A:Glu60 2.61 Cd CB A:Glu60 4.94 Cd OE2 A:Glu60 4.16 Cd CD A:Glu60 3.72 Cd CG A:Glu60 4.95 Cd OE2 A:Glu136 4.55 interactive model: Cadmium binding site 7 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 2v2o. 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: Hoh2022, A: Hoh2026, conact list: Atom Atom Distance (A) Cd CB A:Ser9 4.69 Cd OG1 A:Thr10 4.15 Cd OE1 A:Glu11 2.59 Cd OE2 A:Glu11 2.60 Cd CD A:Glu11 2.98 Cd CG A:Glu11 4.53 Cd NE2 A:Gln120 4.72 Cd OE1 A:Gln120 4.44 Cd CD A:Gln120 4.96 Cd O A:Hoh2022 3.36 Cd O A:Hoh2026 4.90 interactive model: Cadmium binding site 8 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 2v2o. 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: Hoh2074, A: Hoh2076, conact list: Atom Atom Distance (A) Cd OE1 A:Glu53 2.66 Cd OE2 A:Glu53 2.79 Cd CD A:Glu53 3.07 Cd CG A:Glu53 4.55 Cd OE1 A:Glu56 2.33 Cd CB A:Glu56 4.97 Cd OE2 A:Glu56 3.15 Cd CD A:Glu56 3.07 Cd CG A:Glu56 4.54 Cd O A:Hoh2074 3.84 Cd O A:Hoh2076 4.00 interactive model: Cadmium binding site 9 out of 9 in 2v2o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 2v2o. 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: Glu45, conact list: Atom Atom Distance (A) Cd OE1 A:Glu45 2.79 Cd OE2 A:Glu45 2.48 Cd CD A:Glu45 2.94 Cd CG A:Glu45 4.43 interactive model: