Cadmium in the structure of Asv Integrase Core Domain With Cd(II) Cofactors (pdb 1vsj)

The binding sites of Cadmium atom in the structure of Asv Integrase Core Domain With Cd(II) Cofactors (pdb code 1vsj). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1vsj structure was solved by G.BUJACZ, J.ALEXANDRATOS, A.WLODAWER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.1 Space group P43212 a (A) 66.330 b (A) 66.330 c (A) 80.920 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Cadmium Binding Sites: Cadmium binding site 1 out of 2 in 1vsj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1vsj. 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: Asp64, A: Phe65, A: Asp121, A: Cd290, A: Hoh281, A: Hoh282, A: Hoh283, A: Hoh284, A: Hoh292, A: Hoh308, A: Hoh398, A: Hoh405, A: Hoh414, conact list: Atom Atom Distance (A) Cd CB A:Asp64 4.72 Cd OD2 A:Asp64 3.56 Cd OD1 A:Asp64 2.44 Cd CG A:Asp64 3.32 Cd O A:Phe65 4.29 Cd N A:Phe65 4.57 Cd CB A:Asp121 4.62 Cd OD2 A:Asp121 2.33 Cd OD1 A:Asp121 3.65 Cd CG A:Asp121 3.32 Cd CD A:Cd290 4.05 Cd O A:Hoh281 2.30 Cd O A:Hoh282 2.89 Cd O A:Hoh283 2.56 Cd O A:Hoh284 2.06 Cd O A:Hoh292 4.54 Cd O A:Hoh308 3.96 Cd O A:Hoh398 4.44 Cd O A:Hoh405 3.77 Cd O A:Hoh414 4.25 interactive model: Cadmium binding site 2 out of 2 in 1vsj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1vsj. 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: Asp64, A: Phe65, A: Glu157, A: Asn160, A: Cd280, A: Hoh281, A: Hoh283, A: Hoh291, A: Hoh292, A: Hoh307, A: Hoh332, A: Hoh405, A: Hoh414, conact list: Atom Atom Distance (A) Cd CB A:Asp64 4.64 Cd OD2 A:Asp64 2.34 Cd OD1 A:Asp64 4.03 Cd CG A:Asp64 3.46 Cd O A:Phe65 4.34 Cd OE1 A:Glu157 2.46 Cd OE2 A:Glu157 2.69 Cd CD A:Glu157 2.95 Cd CG A:Glu157 4.44 Cd ND2 A:Asn160 3.74 Cd CD A:Cd280 4.05 Cd O A:Hoh281 4.53 Cd O A:Hoh283 1.97 Cd O A:Hoh291 3.64 Cd O A:Hoh292 2.68 Cd O A:Hoh307 4.48 Cd O A:Hoh332 4.80 Cd O A:Hoh405 4.21 Cd O A:Hoh414 4.35 interactive model: