Cadmium in the structure of Crystal Structure of Human Phosphoribosyl Pyrophosphate Synthetase 1 in Complex With Amp(Atp), Cadmium and Sulfate Ion (pdb 2hcr)

The binding sites of Cadmium atom in the structure of Crystal Structure of Human Phosphoribosyl Pyrophosphate Synthetase 1 in Complex With Amp(Atp), Cadmium and Sulfate Ion (pdb code 2hcr). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2hcr structure was solved by S.LI, B.PENG, J.DING, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.2 Space group H3 a (A) 170.236 b (A) 170.236 c (A) 61.820 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.5 Rfree (%) 25.4 Cadmium Binding Sites: Cadmium binding site 1 out of 2 in 2hcr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2hcr. 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: His130, A: Asp171, A: Gly174, A: Arg177, A: Asp220, A: Asp221, A: Amp3001, conact list: Atom Atom Distance (A) Cd CE1 A:His130 4.68 Cd CB A:Asp171 4.67 Cd OD2 A:Asp171 2.99 Cd OD1 A:Asp171 2.62 Cd CG A:Asp171 3.17 Cd N A:Gly174 4.59 Cd CA A:Gly174 4.86 Cd NH1 A:Arg177 4.55 Cd OD2 A:Asp220 3.21 Cd OD1 A:Asp220 3.12 Cd CG A:Asp220 3.57 Cd OD2 A:Asp221 4.37 Cd O3P A:Amp3001 4.64 interactive model: Cadmium binding site 2 out of 2 in 2hcr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2hcr. 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: His130, B: Asp171, B: Gly173, B: Gly174, B: Asp220, B: Asp221, B: Hoh3084, conact list: Atom Atom Distance (A) Cd CE1 B:His130 4.81 Cd CB B:Asp171 4.49 Cd OD2 B:Asp171 2.48 Cd OD1 B:Asp171 2.76 Cd CG B:Asp171 2.98 Cd C B:Gly173 4.57 Cd CA B:Gly173 4.99 Cd N B:Gly174 4.17 Cd CA B:Gly174 4.38 Cd CB B:Asp220 4.78 Cd OD2 B:Asp220 3.17 Cd OD1 B:Asp220 2.66 Cd CG B:Asp220 3.29 Cd OD1 B:Asp221 3.99 Cd O B:Hoh3084 4.99 interactive model: