Vanadium in the structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed With Vanadate, Octopamine, and Tetranucleotide Agtc (pdb 1rgt)

The binding sites of Vanadium atom in the structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed With Vanadate, Octopamine, and Tetranucleotide Agtc (pdb code 1rgt). This binding sites where shown with 5.0 Angstroms radius around Vanadium atom. The 1rgt structure was solved by D.R.DAVIES, H.INTERTHAL, J.J.CHAMPOUX, W.G.HOL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.0 Space group P212121 a (A) 49.791 b (A) 104.894 c (A) 194.124 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 22.8 Vanadium Binding Sites: Vanadium binding site 1 out of 2 in 1rgt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Vanadium in the PDB 1rgt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Vanadium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Dc806, A: Tyr204, A: His263, A: Lys265, A: Asn283, A: His493, A: Lys495, A: Asn516, A: Vo4699, A: Ots995, A: Otr996, A: Hoh752, conact list: Atom Atom Distance (A) V C3' D:Dc806 2.86 V C1' D:Dc806 4.70 V O3' D:Dc806 1.81 V C2' D:Dc806 3.75 V C4' D:Dc806 4.05 V CE2 A:Tyr204 4.76 V CD2 A:Tyr204 4.30 V NE2 A:His263 2.06 V ND1 A:His263 4.14 V CD2 A:His263 3.07 V CE1 A:His263 3.02 V CG A:His263 4.20 V CE A:Lys265 4.42 V NZ A:Lys265 4.14 V ND2 A:Asn283 4.28 V NE2 A:His493 3.46 V CD2 A:His493 4.65 V CE1 A:His493 3.82 V CE A:Lys495 4.72 V NZ A:Lys495 4.37 V ND2 A:Asn516 4.13 V O1 A:Vo4699 1.51 V O3 A:Vo4699 1.52 V V A:Vo4699 0.00 V C5 A:Ots995 4.12 V C4 A:Ots995 3.03 V C3 A:Ots995 3.53 V O4 A:Ots995 2.02 V C2 A:Ots995 4.84 V C5 A:Otr996 4.12 V C4 A:Otr996 3.03 V C3 A:Otr996 3.53 V O4 A:Otr996 2.02 V C2 A:Otr996 4.84 V O A:Hoh752 3.98 interactive model: Vanadium binding site 2 out of 2 in 1rgt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Vanadium in the PDB 1rgt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Vanadium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: Dc806, B: Tyr204, B: His263, B: Lys265, B: Asn283, B: His493, B: Lys495, B: Asn516, B: Vo4699, B: Ots997, B: Otr998, B: Hoh816, conact list: Atom Atom Distance (A) V C3' F:Dc806 2.94 V C1' F:Dc806 4.69 V O3' F:Dc806 1.95 V C2' F:Dc806 3.89 V C4' F:Dc806 4.14 V CE2 B:Tyr204 4.76 V CD2 B:Tyr204 4.28 V NE2 B:His263 2.02 V ND1 B:His263 4.11 V CD2 B:His263 3.04 V CE1 B:His263 2.98 V CG B:His263 4.17 V CE B:Lys265 4.36 V NZ B:Lys265 4.19 V ND2 B:Asn283 4.24 V NE2 B:His493 3.57 V CD2 B:His493 4.78 V CE1 B:His493 3.86 V CE B:Lys495 4.68 V NZ B:Lys495 4.36 V ND2 B:Asn516 4.15 V O1 B:Vo4699 1.47 V O3 B:Vo4699 1.52 V V B:Vo4699 0.00 V C5 B:Ots997 4.15 V C4 B:Ots997 3.06 V C3 B:Ots997 3.56 V O4 B:Ots997 2.06 V C2 B:Ots997 4.88 V C5 B:Otr998 4.15 V C4 B:Otr998 3.06 V C3 B:Otr998 3.56 V O4 B:Otr998 2.06 V C2 B:Otr998 4.88 V O B:Hoh816 4.00 interactive model: