Vanadium in PDB 1rg1: Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtt

The structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtt, PDB code: 1rg1 was solved by D.R.Davies, H.Interthal, J.J.Champoux, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.800, 104.711, 193.751, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.9

The binding sites of Vanadium atom in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtt (pdb code 1rg1). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtt, PDB code: 1rg1:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtt


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtt within 5.0Å range: probe atom residue distance (Å) B Occ A:V699 b:20.2 occ:1.00 V A:VO4699 0.0 20.2 1.0 O3 A:VO4699 1.5 21.1 1.0 O1 A:VO4699 1.5 13.8 1.0 O3' D:DT806 1.9 20.7 1.0 O4 A:OTS997 2.0 20.7 1.0 NE2 A:HIS263 2.0 18.7 1.0 CE1 A:HIS263 2.9 20.0 1.0 C3' D:DT806 2.9 24.1 1.0 C4 A:OTS997 3.0 23.5 1.0 CD2 A:HIS263 3.0 19.5 1.0 NE2 A:HIS493 3.4 19.8 1.0 C3 A:OTS997 3.5 24.9 1.0 CE1 A:HIS493 3.8 17.6 1.0 C2' D:DT806 3.8 25.4 1.0 O A:HOH706 3.9 23.7 1.0 ND1 A:HIS263 4.1 21.0 1.0 C4' D:DT806 4.1 24.1 1.0 CG A:HIS263 4.1 22.5 1.0 C5 A:OTS997 4.1 21.4 1.0 ND2 A:ASN516 4.1 14.9 1.0 NZ A:LYS265 4.2 21.3 1.0 CD2 A:TYR204 4.4 26.1 1.0 CE A:LYS265 4.4 23.9 1.0 NZ A:LYS495 4.5 16.1 1.0 ND2 A:ASN283 4.5 22.8 1.0 CD2 A:HIS493 4.6 18.5 1.0 C1' D:DT806 4.6 26.1 1.0 CE A:LYS495 4.7 17.4 1.0 C2 A:OTS997 4.8 26.2 1.0 CE2 A:TYR204 4.9 25.9 1.0 ND1 A:HIS493 5.0 16.9 1.0

Vanadium binding site 2 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtt


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtt within 5.0Å range: probe atom residue distance (Å) B Occ B:V699 b:21.3 occ:1.00 V B:VO4699 0.0 21.3 1.0 O1 B:VO4699 1.5 17.6 1.0 O3 B:VO4699 1.5 17.2 1.0 O3' F:DT806 1.9 17.7 1.0 NE2 B:HIS263 2.0 18.3 1.0 O4 B:OTS998 2.1 21.8 1.0 C3' F:DT806 2.9 18.9 1.0 CE1 B:HIS263 2.9 18.9 1.0 CD2 B:HIS263 3.0 17.8 1.0 C4 B:OTS998 3.1 21.0 1.0 C3 B:OTS998 3.5 23.5 1.0 NE2 B:HIS493 3.5 20.3 1.0 C2' F:DT806 3.8 20.7 1.0 CE1 B:HIS493 3.8 19.5 1.0 O B:HOH676 3.9 23.6 1.0 ND1 B:HIS263 4.1 18.1 1.0 ND2 B:ASN516 4.1 17.7 1.0 C4' F:DT806 4.1 19.8 1.0 NZ B:LYS265 4.1 16.3 1.0 CG B:HIS263 4.1 17.6 1.0 C5 B:OTS998 4.2 22.6 1.0 ND2 B:ASN283 4.3 14.1 1.0 CE B:LYS265 4.3 19.0 1.0 NZ B:LYS495 4.4 14.1 1.0 CD2 B:TYR204 4.4 24.4 1.0 C1' F:DT806 4.6 22.0 1.0 CE B:LYS495 4.7 15.8 1.0 CD2 B:HIS493 4.7 18.0 1.0 C2 B:OTS998 4.8 25.4 1.0 O4' F:DT806 4.9 20.3 1.0 CE2 B:TYR204 4.9 26.6 1.0

D.R.Davies, H.Interthal, J.J.Champoux, W.G.Hol. Explorations of Peptide and Oligonucleotide Binding Sites of Tyrosyl-Dna Phosphodiesterase Using Vanadate Complexes. J.Med.Chem. V. 47 829 2004.
ISSN: ISSN 0022-2623
PubMed: 14761185
DOI: 10.1021/JM030487X