Vanadium in PDB 1rfi: Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Pentapeptide Klnyk, and Tetranucleotide Agtc

The structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Pentapeptide Klnyk, and Tetranucleotide Agtc, PDB code: 1rfi 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 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.820, 104.832, 193.539, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.7

The binding sites of Vanadium atom in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Pentapeptide Klnyk, and Tetranucleotide Agtc (pdb code 1rfi). 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, Pentapeptide Klnyk, and Tetranucleotide Agtc, PDB code: 1rfi:
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, Pentapeptide Klnyk, and Tetranucleotide Agtc


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, Pentapeptide Klnyk, and Tetranucleotide Agtc within 5.0Å range: probe atom residue distance (Å) B Occ A:V699 b:20.1 occ:1.00 V A:VO4699 0.0 20.1 1.0 O1 A:VO4699 1.5 16.7 1.0 O3 A:VO4699 1.5 20.8 1.0 O3' D:DC806 1.8 18.7 1.0 OH C:TYR723 2.0 23.8 1.0 NE2 A:HIS263 2.1 19.0 1.0 C3' D:DC806 2.9 21.3 1.0 CE1 A:HIS263 3.0 15.3 1.0 CZ C:TYR723 3.1 31.2 1.0 CD2 A:HIS263 3.1 18.4 1.0 NE2 A:HIS493 3.5 14.1 1.0 CE2 C:TYR723 3.7 31.3 1.0 C2' D:DC806 3.9 23.6 1.0 O A:HOH752 3.9 22.5 1.0 CE1 A:HIS493 4.0 11.8 1.0 CE1 C:TYR723 4.1 31.9 1.0 C4' D:DC806 4.1 22.3 1.0 ND1 A:HIS263 4.1 17.7 1.0 ND2 A:ASN516 4.2 17.2 1.0 CG A:HIS263 4.2 18.7 1.0 NZ A:LYS265 4.3 15.7 1.0 CD2 A:TYR204 4.3 23.6 1.0 ND2 A:ASN283 4.4 17.2 1.0 NZ A:LYS495 4.4 17.1 1.0 CE A:LYS265 4.5 15.2 1.0 CD2 A:HIS493 4.7 14.4 1.0 C1' D:DC806 4.7 24.6 1.0 CE A:LYS495 4.8 16.2 1.0 CE2 A:TYR204 4.8 24.9 1.0 CD2 C:TYR723 5.0 35.2 1.0 OD1 A:ASN283 5.0 20.2 1.0 O4' D:DC806 5.0 22.6 1.0

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


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, Pentapeptide Klnyk, and Tetranucleotide Agtc within 5.0Å range: probe atom residue distance (Å) B Occ B:V699 b:17.7 occ:1.00 V B:VO4699 0.0 17.7 1.0 O1 B:VO4699 1.5 17.2 1.0 O3 B:VO4699 1.5 15.8 1.0 O3' F:DC806 1.8 16.9 1.0 OH E:TYR723 1.9 25.2 1.0 NE2 B:HIS263 2.0 9.8 1.0 C3' F:DC806 2.9 16.9 1.0 CE1 B:HIS263 2.9 11.7 1.0 CD2 B:HIS263 3.0 14.8 1.0 CZ E:TYR723 3.0 29.0 1.0 CE1 E:TYR723 3.6 31.1 1.0 NE2 B:HIS493 3.7 16.1 1.0 C2' F:DC806 3.7 20.8 1.0 O B:HOH816 3.8 16.3 1.0 CE1 B:HIS493 4.0 16.8 1.0 NZ B:LYS265 4.0 12.5 1.0 C4' F:DC806 4.0 19.6 1.0 CE2 E:TYR723 4.1 29.4 1.0 ND1 B:HIS263 4.1 13.5 1.0 CG B:HIS263 4.1 14.3 1.0 ND2 B:ASN516 4.1 15.3 1.0 CE B:LYS265 4.3 18.0 1.0 CD2 B:TYR204 4.3 20.2 1.0 NZ B:LYS495 4.4 10.9 1.0 ND2 B:ASN283 4.4 13.6 1.0 C1' F:DC806 4.6 21.0 1.0 CE B:LYS495 4.7 12.2 1.0 CE2 B:TYR204 4.8 22.4 1.0 CD2 B:HIS493 4.8 14.8 1.0 O4' F:DC806 4.9 20.7 1.0 CD1 E:TYR723 4.9 31.2 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