Cadmium in the structure of X-Ray Structure of Human Ubiquitin Cd(II) Adduct (pdb 3eec)

The binding sites of Cadmium atom in the structure of X-Ray Structure of Human Ubiquitin Cd(II) Adduct (pdb code 3eec). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3eec structure was solved by G.FALINI, S.FERMANI, G.TOSI, F.ARNESANO, G.NATILE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 74.4-3.0 Space group P4332 a (A) 105.253 b (A) 105.253 c (A) 105.253 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 27.9 Rfree (%) 30 Cadmium Binding Sites: Cadmium binding site 1 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3eec. 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: Lys63, A: Glu64, A: Hoh107, A: Hoh108, conact list: Atom Atom Distance (A) Cd CE A:Lys63 4.12 Cd CD A:Lys63 4.84 Cd OE1 A:Glu64 2.33 Cd OE2 A:Glu64 2.54 Cd CD A:Glu64 2.77 Cd CG A:Glu64 4.29 Cd O A:Hoh107 2.56 Cd O A:Hoh108 2.53 interactive model: Cadmium binding site 2 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3eec. 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: Met1, A: Gln2, A: Glu16, conact list: Atom Atom Distance (A) Cd O A:Met1 2.50 Cd N A:Met1 2.66 Cd CB A:Met1 4.69 Cd C A:Met1 3.13 Cd CA A:Met1 3.45 Cd N A:Gln2 4.26 Cd OE1 A:Glu16 2.34 Cd OE2 A:Glu16 2.52 Cd CD A:Glu16 2.66 Cd CG A:Glu16 4.21 interactive model: Cadmium binding site 3 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3eec. 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: Glu18, conact list: Atom Atom Distance (A) Cd OE1 A:Glu18 2.72 Cd OE2 A:Glu18 2.29 Cd CD A:Glu18 2.83 Cd CG A:Glu18 4.32 interactive model: Cadmium binding site 4 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3eec. 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: Thr55, A: Asp58, conact list: Atom Atom Distance (A) Cd N A:Thr55 4.87 Cd CG2 A:Thr55 4.78 Cd OG1 A:Thr55 4.17 Cd CB A:Asp58 4.52 Cd OD2 A:Asp58 2.72 Cd OD1 A:Asp58 2.57 Cd CG A:Asp58 3.00 interactive model: Cadmium binding site 5 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3eec. 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: Glu24, A: Asp39, A: Asp52, A: Cd106, conact list: Atom Atom Distance (A) Cd OE1 A:Glu24 2.36 Cd OE2 A:Glu24 3.23 Cd CD A:Glu24 3.15 Cd CG A:Glu24 4.60 Cd OD1 A:Asp39 3.75 Cd CG A:Asp39 4.82 Cd CB A:Asp52 3.78 Cd OD2 A:Asp52 2.44 Cd OD1 A:Asp52 4.26 Cd CG A:Asp52 3.30 Cd CD A:Cd106 4.03 interactive model: Cadmium binding site 6 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 3eec. 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: Asp39, A: Cd105, conact list: Atom Atom Distance (A) Cd CB A:Asp39 4.43 Cd OD2 A:Asp39 2.75 Cd OD1 A:Asp39 2.48 Cd CG A:Asp39 2.95 Cd CD A:Cd105 4.03 interactive model: Cadmium binding site 7 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 3eec. 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: B: His68, conact list: Atom Atom Distance (A) Cd NE2 B:His68 2.34 Cd ND1 B:His68 4.17 Cd CD2 B:His68 2.98 Cd CE1 B:His68 3.28 Cd CG B:His68 4.06 interactive model: Cadmium binding site 8 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 3eec. 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: B: Met1, B: Gln2, B: Glu16, B: Val17, B: Hoh207, conact list: Atom Atom Distance (A) Cd O B:Met1 2.63 Cd N B:Met1 2.83 Cd CB B:Met1 4.54 Cd C B:Met1 3.16 Cd CA B:Met1 3.15 Cd N B:Gln2 4.31 Cd CB B:Gln2 4.97 Cd OE1 B:Glu16 2.49 Cd OE2 B:Glu16 2.43 Cd CD B:Glu16 2.79 Cd CG B:Glu16 4.27 Cd O B:Val17 4.99 Cd O B:Hoh207 2.34 interactive model: Cadmium binding site 9 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 3eec. 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: B: Glu18, B: Asp21, B: Asn25, B: Lys29, B: Hoh208, B: Hoh209, conact list: Atom Atom Distance (A) Cd N B:Glu18 4.65 Cd OE1 B:Glu18 2.96 Cd CB B:Glu18 4.24 Cd CD B:Glu18 3.94 Cd CG B:Glu18 4.12 Cd CB B:Asp21 4.38 Cd OD2 B:Asp21 2.53 Cd OD1 B:Asp21 2.63 Cd CG B:Asp21 2.90 Cd ND2 B:Asn25 4.46 Cd CE B:Lys29 4.22 Cd NZ B:Lys29 3.14 Cd O B:Hoh208 2.89 Cd O B:Hoh209 2.54 interactive model: Cadmium binding site 10 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 3eec. 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: B: Thr55, B: Asp58, conact list: Atom Atom Distance (A) Cd CG2 B:Thr55 4.55 Cd OG1 B:Thr55 4.55 Cd CB B:Asp58 4.48 Cd OD2 B:Asp58 2.56 Cd OD1 B:Asp58 2.65 Cd CG B:Asp58 2.96 interactive model: Cadmium binding site 11 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Cadmium in the PDB 3eec. 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: B: Glu24, B: Lys27, B: Asp39, B: Asp52, B: Cd206, conact list: Atom Atom Distance (A) Cd OE1 B:Glu24 2.28 Cd OE2 B:Glu24 3.81 Cd CD B:Glu24 3.38 Cd CG B:Glu24 4.66 Cd NZ B:Lys27 4.92 Cd OD2 B:Asp39 3.73 Cd CG B:Asp39 4.96 Cd CB B:Asp52 3.61 Cd OD2 B:Asp52 2.47 Cd OD1 B:Asp52 3.88 Cd CG B:Asp52 3.08 Cd CD B:Cd206 4.35 interactive model: Cadmium binding site 12 out of 12 in 3eec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Cadmium in the PDB 3eec. 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: B: Asp39, B: Cd205, conact list: Atom Atom Distance (A) Cd CB B:Asp39 4.41 Cd OD2 B:Asp39 2.64 Cd OD1 B:Asp39 2.42 Cd CG B:Asp39 2.88 Cd CD B:Cd205 4.35 interactive model: