Vanadium in the structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex With Vanadate, Dna and A Human Topoisomerase I-Derived Peptide (pdb 1nop)

The binding sites of Vanadium atom in the structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase (TDP1) in Complex With Vanadate, Dna and A Human Topoisomerase I-Derived Peptide (pdb code 1nop). This binding sites where shown with 5.0 Angstroms radius around Vanadium atom. The 1nop structure was solved by D.R.DAVIES, H.INTERTHAL, J.J.CHAMPOUX, W.G.J.HOL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 95.3-2.3 Space group P212121 a (A) 49.803 b (A) 104.719 c (A) 193.924 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.6 Rfree (%) 25.2 Vanadium Binding Sites: Vanadium binding site 1 out of 2 in 1nop Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Vanadium in the PDB 1nop. 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: Dt806, A: Tyr204, A: His263, A: Lys265, A: Asn283, A: His493, A: Lys495, A: Asn516, C: Tyr723, A: Vo4699, A: Hoh728, conact list: Atom Atom Distance (A) V C3' D:Dt806 2.95 V C1' D:Dt806 4.69 V O3' D:Dt806 1.77 V O4' D:Dt806 4.98 V C2' D:Dt806 3.87 V C4' D:Dt806 4.09 V CE2 A:Tyr204 4.83 V CD2 A:Tyr204 4.41 V NE2 A:His263 2.04 V ND1 A:His263 4.10 V CD2 A:His263 3.10 V CE1 A:His263 2.96 V CG A:His263 4.20 V CE A:Lys265 4.34 V NZ A:Lys265 4.22 V ND2 A:Asn283 4.27 V NE2 A:His493 3.43 V ND1 A:His493 4.94 V CD2 A:His493 4.61 V CE1 A:His493 3.73 V CE A:Lys495 4.57 V NZ A:Lys495 4.33 V ND2 A:Asn516 4.01 V CE2 C:Tyr723 3.64 V CD2 C:Tyr723 4.98 V CZ C:Tyr723 3.08 V CE1 C:Tyr723 4.11 V OH C:Tyr723 1.99 V O1 A:Vo4699 1.60 V O3 A:Vo4699 1.68 V V A:Vo4699 0.00 V O A:Hoh728 3.75 interactive model: Vanadium binding site 2 out of 2 in 1nop Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Vanadium in the PDB 1nop. 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: Dt806, B: Tyr204, B: His263, B: Lys265, B: Asn283, B: His493, B: Lys495, B: Asn516, B: Vo4699, conact list: Atom Atom Distance (A) V C3' F:Dt806 2.81 V C1' F:Dt806 4.55 V O3' F:Dt806 1.75 V O4' F:Dt806 4.77 V C2' F:Dt806 3.69 V C4' F:Dt806 3.98 V CE2 B:Tyr204 4.96 V CD2 B:Tyr204 4.43 V NE2 B:His263 2.17 V ND1 B:His263 4.20 V CD2 B:His263 3.26 V CE1 B:His263 3.03 V CG B:His263 4.34 V CE B:Lys265 4.30 V NZ B:Lys265 4.14 V ND2 B:Asn283 4.32 V NE2 B:His493 3.53 V CD2 B:His493 4.67 V CE1 B:His493 3.92 V CE B:Lys495 4.61 V NZ B:Lys495 4.29 V ND2 B:Asn516 4.09 V O1 B:Vo4699 1.52 V O3 B:Vo4699 1.66 V V B:Vo4699 0.00 interactive model: