Cadmium in the structure of Anomalous Substructure of Apoferritin (pdb 2g4h)

The binding sites of Cadmium atom in the structure of Anomalous Substructure of Apoferritin (pdb code 2g4h). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2g4h structure was solved by C.MUELLER-DIECKMANN, M.S.WEISS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.0 Space group F432 a (A) 182.160 b (A) 182.160 c (A) 182.160 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.5 Rfree (%) 21.8 Cadmium Binding Sites: Cadmium binding site 1 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2g4h. 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: Gln86, A: Lys87, conact list: Atom Atom Distance (A) Cd NE2 A:Gln86 3.86 Cd OE1 A:Gln86 2.35 Cd CB A:Gln86 4.96 Cd CD A:Gln86 3.40 Cd CG A:Gln86 4.70 Cd CA A:Gln86 4.98 Cd N A:Lys87 4.99 interactive model: Cadmium binding site 2 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2g4h. 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: Glu60, A: Glu61, A: Glu64, A: Hoh229, conact list: Atom Atom Distance (A) Cd OE1 A:Glu60 2.19 Cd CB A:Glu60 4.90 Cd OE2 A:Glu60 4.29 Cd CD A:Glu60 3.15 Cd CG A:Glu60 3.47 Cd OE1 A:Glu61 4.49 Cd OE2 A:Glu61 2.90 Cd CD A:Glu61 4.05 Cd OE1 A:Glu64 2.73 Cd OE2 A:Glu64 2.14 Cd CD A:Glu64 2.76 Cd CG A:Glu64 4.27 Cd O A:Hoh229 4.32 interactive model: Cadmium binding site 3 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2g4h. 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: Asp131, A: Glu134, A: Ser135, A: Cd204, conact list: Atom Atom Distance (A) Cd O A:Asp131 4.87 Cd CB A:Asp131 4.91 Cd OD1 A:Asp131 2.87 Cd CG A:Asp131 4.12 Cd CA A:Asp131 4.95 Cd OE1 A:Glu134 4.08 Cd CB A:Glu134 4.77 Cd OG A:Ser135 3.75 Cd CD A:Cd204 4.50 interactive model: Cadmium binding site 4 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2g4h. 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: Asp131, A: Glu134, A: Cd203, A: Hoh306, conact list: Atom Atom Distance (A) Cd N A:Asp131 4.80 Cd CA A:Asp131 4.71 Cd OE1 A:Glu134 2.40 Cd OE2 A:Glu134 3.41 Cd CD A:Glu134 3.27 Cd CG A:Glu134 4.70 Cd CD A:Cd203 4.50 Cd O A:Hoh306 1.42 interactive model: Cadmium binding site 5 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2g4h. 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: Hoh229, conact list: Atom Atom Distance (A) Cd CG A:Glu57 4.68 Cd OE1 A:Glu60 3.52 Cd OE2 A:Glu60 2.59 Cd CD A:Glu60 3.37 Cd CG A:Glu60 4.74 Cd O A:Hoh229 4.11 interactive model: Cadmium binding site 6 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2g4h. 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: Ser13, A: Thr14, A: Glu15, A: Gln124, A: Hoh275, conact list: Atom Atom Distance (A) Cd CB A:Ser13 4.66 Cd N A:Thr14 5.00 Cd OG1 A:Thr14 4.01 Cd OE1 A:Glu15 2.53 Cd OE2 A:Glu15 2.57 Cd CD A:Glu15 2.91 Cd CG A:Glu15 4.44 Cd NE2 A:Gln124 4.48 Cd OE1 A:Gln124 4.52 Cd CD A:Gln124 4.88 Cd O A:Hoh275 3.34 interactive model: Cadmium binding site 7 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 2g4h. 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: Glu49, A: Hoh233, conact list: Atom Atom Distance (A) Cd OE1 A:Glu49 2.33 Cd OE2 A:Glu49 2.91 Cd CD A:Glu49 2.90 Cd CG A:Glu49 4.35 Cd O A:Hoh233 4.24 interactive model: Cadmium binding site 8 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 2g4h. 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: Arg43, A: Glu92, conact list: Atom Atom Distance (A) Cd NH2 A:Arg43 4.58 Cd NH1 A:Arg43 4.78 Cd OE1 A:Glu92 3.01 Cd OE2 A:Glu92 2.23 Cd CD A:Glu92 2.94 Cd CG A:Glu92 4.40 interactive model: Cadmium binding site 9 out of 9 in 2g4h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 2g4h. 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: Asp42, A: Glu49, A: Cys52, A: Hoh224, conact list: Atom Atom Distance (A) Cd CB A:Asp42 3.74 Cd OD2 A:Asp42 4.61 Cd OD1 A:Asp42 2.87 Cd CG A:Asp42 3.56 Cd CA A:Asp42 4.31 Cd O A:Glu49 5.00 Cd CG A:Glu49 4.53 Cd CA A:Glu49 4.83 Cd CB A:Cys52 3.80 Cd SG A:Cys52 3.13 Cd O A:Hoh224 3.63 interactive model: