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

The structure of The Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtg, PDB code: 1rgu 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 / 2.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.716, 104.557, 193.180, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.1

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

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


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of The Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtg within 5.0Å range: probe atom residue distance (Å) B Occ A:V699 b:20.9 occ:1.00 V A:VO4699 0.0 20.9 1.0 O1 A:VO4699 1.5 15.4 1.0 O3 A:VO4699 1.5 20.6 1.0 O3' D:DG806 1.8 18.1 1.0 O4 A:OTS995 1.9 18.6 1.0 NE2 A:HIS263 2.0 18.2 1.0 C3' D:DG806 2.8 21.8 1.0 CD2 A:HIS263 3.0 18.1 1.0 C4 A:OTS995 3.0 24.6 1.0 CE1 A:HIS263 3.0 15.7 1.0 C3 A:OTS995 3.4 25.7 1.0 NE2 A:HIS493 3.6 15.8 1.0 C2' D:DG806 3.7 22.9 1.0 CE1 A:HIS493 3.9 14.4 1.0 O A:HOH706 3.9 23.9 1.0 C4' D:DG806 4.0 22.9 1.0 ND1 A:HIS263 4.1 17.6 1.0 CG A:HIS263 4.1 19.6 1.0 ND2 A:ASN516 4.1 18.9 1.0 C5 A:OTS995 4.2 24.8 1.0 NZ A:LYS265 4.2 22.1 1.0 CD2 A:TYR204 4.4 25.5 1.0 CE A:LYS265 4.4 20.5 1.0 NZ A:LYS495 4.5 20.5 1.0 ND2 A:ASN283 4.5 26.1 1.0 C1' D:DG806 4.6 23.4 1.0 CE A:LYS495 4.7 24.0 1.0 CD2 A:HIS493 4.8 15.2 1.0 C2 A:OTS995 4.8 28.2 1.0 O4' D:DG806 4.8 23.3 1.0 CE2 A:TYR204 4.8 27.2 1.0 OD1 A:ASN283 5.0 25.1 1.0

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


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of The Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtg within 5.0Å range: probe atom residue distance (Å) B Occ B:V699 b:21.6 occ:1.00 V B:VO4699 0.0 21.6 1.0 O1 B:VO4699 1.5 22.1 1.0 O3 B:VO4699 1.5 17.6 1.0 O3' F:DG806 1.8 17.1 1.0 O4 B:OTS996 2.0 28.8 1.0 NE2 B:HIS263 2.0 15.4 1.0 C3' F:DG806 2.8 17.9 1.0 CE1 B:HIS263 2.9 14.8 1.0 CD2 B:HIS263 3.1 16.3 1.0 C4 B:OTS996 3.1 28.4 1.0 C3 B:OTS996 3.6 30.7 1.0 NE2 B:HIS493 3.6 20.2 1.0 C2' F:DG806 3.7 19.8 1.0 O B:HOH676 3.9 22.2 1.0 CE1 B:HIS493 3.9 21.1 1.0 ND2 B:ASN516 4.0 18.3 1.0 C4' F:DG806 4.0 18.5 1.0 ND1 B:HIS263 4.0 16.4 1.0 CG B:HIS263 4.2 17.2 1.0 NZ B:LYS265 4.2 17.3 1.0 C5 B:OTS996 4.2 27.4 1.0 CE B:LYS265 4.3 20.4 1.0 NZ B:LYS495 4.3 14.0 1.0 ND2 B:ASN283 4.4 18.2 1.0 CD2 B:TYR204 4.5 28.3 1.0 CE B:LYS495 4.5 14.6 1.0 C1' F:DG806 4.7 22.4 1.0 CD2 B:HIS493 4.8 17.3 1.0 C2 B:OTS996 5.0 31.5 1.0 O4' F:DG806 5.0 20.7 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