Cadmium in the structure of Complex of Equine Apoferritin With the H-Diaziflurane Photolabeling Reagent (pdb 2gyd)

The binding sites of Cadmium atom in the structure of Complex of Equine Apoferritin With the H-Diaziflurane Photolabeling Reagent (pdb code 2gyd). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2gyd structure was solved by P.J.LOLL, M.J.ROSSI, R.ECKENHOFF, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 37.1-1.7 Space group F432 a (A) 181.890 b (A) 181.890 c (A) 181.890 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.7 Rfree (%) 21.7 Cadmium Binding Sites: Cadmium binding site 1 out of 7 in 2gyd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2gyd. 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: Hoh1008, A: Hoh1061, A: Hoh1064, conact list: Atom Atom Distance (A) Cd CB A:Asp80 4.28 Cd OD2 A:Asp80 2.33 Cd OD1 A:Asp80 2.52 Cd CG A:Asp80 2.77 Cd O A:Hoh1008 4.22 Cd O A:Hoh1061 4.54 Cd O A:Hoh1064 4.59 interactive model: Cadmium binding site 2 out of 7 in 2gyd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2gyd. 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: His114, A: Cys126, A: Glu130, A: Cd1006, A: Cd1007, conact list: Atom Atom Distance (A) Cd NE2 A:His114 4.40 Cd SG A:Cys126 3.75 Cd OE1 A:Glu130 3.02 Cd OE2 A:Glu130 2.41 Cd CD A:Glu130 3.07 Cd CG A:Glu130 4.56 Cd CD A:Cd1006 3.62 Cd CD A:Cd1007 3.16 interactive model: Cadmium binding site 3 out of 7 in 2gyd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2gyd. 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: Hoh1184, conact list: Atom Atom Distance (A) Cd OE1 A:Glu53 2.57 Cd OE2 A:Glu53 3.21 Cd CD A:Glu53 3.26 Cd CG A:Glu53 4.74 Cd OE1 A:Glu56 2.59 Cd CB A:Glu56 4.97 Cd OE2 A:Glu56 3.23 Cd CD A:Glu56 3.22 Cd CG A:Glu56 4.61 Cd O A:Hoh1184 3.71 interactive model: Cadmium binding site 4 out of 7 in 2gyd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2gyd. 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: Arg39, A: Glu88, A: Hoh1009, A: Hoh1117, conact list: Atom Atom Distance (A) Cd NH2 A:Arg39 4.33 Cd NH1 A:Arg39 4.73 Cd OE1 A:Glu88 2.55 Cd CB A:Glu88 4.99 Cd OE2 A:Glu88 2.51 Cd CD A:Glu88 2.85 Cd CG A:Glu88 4.34 Cd O A:Hoh1009 4.25 Cd O A:Hoh1117 3.54 interactive model: Cadmium binding site 5 out of 7 in 2gyd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2gyd. 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: Hoh1010, A: Hoh1067, A: Hoh1156, A: Hoh1184, conact list: Atom Atom Distance (A) Cd OE2 A:Glu56 3.21 Cd CD A:Glu56 4.02 Cd CG A:Glu56 4.12 Cd OE1 A:Glu57 2.66 Cd OE2 A:Glu57 3.78 Cd CD A:Glu57 3.56 Cd CG A:Glu57 4.89 Cd OE1 A:Glu60 2.96 Cd OE2 A:Glu60 2.42 Cd CD A:Glu60 3.03 Cd CG A:Glu60 4.49 Cd O A:Hoh1010 4.40 Cd O A:Hoh1067 3.31 Cd O A:Hoh1156 2.08 Cd O A:Hoh1184 3.99 interactive model: Cadmium binding site 6 out of 7 in 2gyd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2gyd. 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: His114, A: Ser118, A: Cys126, A: Glu130, A: Cd1002, A: Hoh1174, conact list: Atom Atom Distance (A) Cd NE2 A:His114 2.10 Cd ND1 A:His114 3.83 Cd CD2 A:His114 3.28 Cd CE1 A:His114 2.64 Cd CG A:His114 4.16 Cd CB A:Ser118 4.76 Cd OG A:Ser118 3.49 Cd CB A:Cys126 3.54 Cd SG A:Cys126 2.62 Cd CA A:Cys126 4.62 Cd OE2 A:Glu130 3.69 Cd CD A:Glu130 4.63 Cd CD A:Cd1002 3.62 Cd O A:Hoh1174 3.29 interactive model: Cadmium binding site 7 out of 7 in 2gyd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 2gyd. 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: Glu130, A: Cd1002, A: Hoh1158, conact list: Atom Atom Distance (A) Cd SG A:Cys126 4.31 Cd OE1 A:Glu130 2.49 Cd CB A:Glu130 4.92 Cd OE2 A:Glu130 4.02 Cd CD A:Glu130 3.55 Cd CG A:Glu130 4.74 Cd CD A:Cd1002 3.16 Cd O A:Hoh1158 3.87 interactive model: