Cadmium in the structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met) (pdb 1q8a)

The binding sites of Cadmium atom in the structure of Cobalamin-Dependent Methionine Synthase (1-566) From Thermotoga Maritima (CD2+:L-Hcy Complex, Se-Met) (pdb code 1q8a). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1q8a structure was solved by J.C.EVANS, D.P.HUDDLER, M.T.HILGERS, G.ROMANCHUK, R.G.MATTHEWS, M.L.LUDWIG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.7 Space group P1211 a (A) 59.120 b (A) 86.190 c (A) 126.080 alpha (°) 90.00 beta (°) 99.99 gamma (°) 90.00 Rfactor (%) 21.4 Rfree (%) 24.2 Cadmium Binding Sites: Cadmium binding site 1 out of 2 in 1q8a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1q8a. 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: Thr147, A: Asn206, A: Cys207, A: Asn234, A: Cys272, A: Cys273, A: Hcs701, conact list: Atom Atom Distance (A) Cd OG1 A:Thr147 4.75 Cd ND2 A:Asn206 4.43 Cd N A:Cys207 4.97 Cd CB A:Cys207 3.41 Cd SG A:Cys207 2.68 Cd CA A:Cys207 4.33 Cd OD1 A:Asn234 4.01 Cd CB A:Cys272 3.76 Cd SG A:Cys272 2.39 Cd C A:Cys272 4.59 Cd CA A:Cys272 4.63 Cd N A:Cys273 3.59 Cd CB A:Cys273 3.66 Cd SG A:Cys273 2.61 Cd CA A:Cys273 4.22 Cd CB A:Hcs701 3.90 Cd CG A:Hcs701 3.45 Cd SD A:Hcs701 2.52 interactive model: Cadmium binding site 2 out of 2 in 1q8a Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1q8a. 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: Thr147, B: Asn206, B: Cys207, B: Asn234, B: Cys272, B: Cys273, B: Hcs702, conact list: Atom Atom Distance (A) Cd OG1 B:Thr147 4.89 Cd ND2 B:Asn206 4.46 Cd CB B:Cys207 3.35 Cd SG B:Cys207 2.45 Cd CA B:Cys207 4.41 Cd OD1 B:Asn234 3.69 Cd CG B:Asn234 4.74 Cd CB B:Cys272 3.75 Cd SG B:Cys272 2.44 Cd C B:Cys272 4.60 Cd CA B:Cys272 4.62 Cd N B:Cys273 3.62 Cd CB B:Cys273 3.69 Cd SG B:Cys273 2.63 Cd CA B:Cys273 4.24 Cd CB B:Hcs702 3.88 Cd CG B:Hcs702 3.41 Cd SD B:Hcs702 2.47 interactive model: