Cadmium in the structure of Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed With Cadmium and Citrate (pdb 2cmv)

The binding sites of Cadmium atom in the structure of Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase Complexed With Cadmium and Citrate (pdb code 2cmv). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2cmv structure was solved by H.J.CHO, K.J.KIM, T.L.HUH, B.S.KANG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.9-2.5 Space group C121 a (A) 98.246 b (A) 91.428 c (A) 109.724 alpha (°) 90.00 beta (°) 113.65 gamma (°) 90.00 Rfactor (%) 18.2 Rfree (%) 24.1 Cadmium Binding Sites: Cadmium binding site 1 out of 2 in 2cmv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2cmv. 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: Arg109, A: Asp275, A: Asp279, A: Ala308, B: Lys212, B: Asp252, A: Nap1415, A: Flc1416, A: Hoh2022, A: Hoh2051, conact list: Atom Atom Distance (A) Cd NH2 A:Arg109 3.88 Cd O A:Asp275 4.10 Cd CB A:Asp275 4.39 Cd OD2 A:Asp275 1.97 Cd C A:Asp275 4.40 Cd OD1 A:Asp275 3.83 Cd CG A:Asp275 3.20 Cd CA A:Asp275 4.41 Cd CB A:Asp279 4.88 Cd OD2 A:Asp279 3.11 Cd OD1 A:Asp279 3.35 Cd CG A:Asp279 3.53 Cd O A:Ala308 3.98 Cd NZ B:Lys212 4.71 Cd CB B:Asp252 4.02 Cd OD2 B:Asp252 2.08 Cd OD1 B:Asp252 3.30 Cd CG B:Asp252 2.89 Cd CA B:Asp252 4.92 Cd C5N A:Nap1415 4.69 Cd C4N A:Nap1415 4.87 Cd OHB A:Flc1416 4.16 Cd OA2 A:Flc1416 3.88 Cd CBC A:Flc1416 4.90 Cd CB A:Flc1416 4.78 Cd CAC A:Flc1416 3.35 Cd CA A:Flc1416 4.56 Cd OA1 A:Flc1416 2.22 Cd OB2 A:Flc1416 4.94 Cd O A:Hoh2022 2.30 Cd O A:Hoh2051 2.29 interactive model: Cadmium binding site 2 out of 2 in 2cmv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2cmv. 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: Lys212, A: Asp252, B: Arg109, B: Asp275, B: Ser278, B: Asp279, B: Ala308, B: Nap1415, B: Flc1416, conact list: Atom Atom Distance (A) Cd NZ A:Lys212 4.73 Cd CB A:Asp252 3.85 Cd OD2 A:Asp252 4.70 Cd OD1 A:Asp252 2.57 Cd CG A:Asp252 3.58 Cd NH2 B:Arg109 3.96 Cd O B:Asp275 4.22 Cd CB B:Asp275 4.75 Cd OD2 B:Asp275 2.46 Cd C B:Asp275 4.59 Cd OD1 B:Asp275 4.31 Cd CG B:Asp275 3.66 Cd CA B:Asp275 4.72 Cd OG B:Ser278 4.88 Cd OD2 B:Asp279 3.18 Cd OD1 B:Asp279 3.27 Cd CG B:Asp279 3.59 Cd O B:Ala308 3.77 Cd C B:Ala308 4.98 Cd C5N B:Nap1415 4.46 Cd C4N B:Nap1415 4.67 Cd OHB B:Flc1416 3.54 Cd OA2 B:Flc1416 1.94 Cd CB B:Flc1416 4.49 Cd CAC B:Flc1416 3.05 Cd CA B:Flc1416 4.29 Cd OA1 B:Flc1416 3.55 interactive model: