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

Protein crystallography data

The structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtc, PDB code: 1rgt 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.791, 104.894, 194.124, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.8

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agtc (pdb code 1rgt). 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 Agtc, PDB code: 1rgt:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 1rgt

Go back to Vanadium Binding Sites List in 1rgt
Vanadium binding site 1 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, 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, Octopamine, and Tetranucleotide Agtc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V699

b:15.3
occ:1.00
V A:VO4699 0.0 15.3 1.0
O1 A:VO4699 1.5 10.8 1.0
O3 A:VO4699 1.5 15.8 1.0
O3' D:DC806 1.8 15.7 1.0
O4 A:OTS995 2.0 19.9 0.5
O4 A:OTR996 2.0 19.9 0.5
NE2 A:HIS263 2.1 13.2 1.0
C3' D:DC806 2.9 15.8 1.0
CE1 A:HIS263 3.0 14.3 1.0
C4 A:OTS995 3.0 20.4 0.5
C4 A:OTR996 3.0 20.4 0.5
CD2 A:HIS263 3.1 13.1 1.0
NE2 A:HIS493 3.5 12.5 1.0
C3 A:OTS995 3.5 21.8 0.5
C3 A:OTR996 3.5 21.8 0.5
C2' D:DC806 3.7 16.1 1.0
CE1 A:HIS493 3.8 12.7 1.0
O A:HOH752 4.0 16.1 1.0
C4' D:DC806 4.1 19.2 1.0
C5 A:OTS995 4.1 18.0 0.5
C5 A:OTR996 4.1 18.0 0.5
ND2 A:ASN516 4.1 15.9 1.0
ND1 A:HIS263 4.1 13.7 1.0
NZ A:LYS265 4.1 15.9 1.0
CG A:HIS263 4.2 15.0 1.0
ND2 A:ASN283 4.3 13.5 1.0
CD2 A:TYR204 4.3 19.4 1.0
NZ A:LYS495 4.4 15.2 1.0
CE A:LYS265 4.4 15.0 1.0
CD2 A:HIS493 4.6 14.3 1.0
C1' D:DC806 4.7 18.5 1.0
CE A:LYS495 4.7 14.7 1.0
CE2 A:TYR204 4.8 20.9 1.0
C2 A:OTS995 4.8 22.0 0.5
C2 A:OTR996 4.8 22.0 0.5

Vanadium binding site 2 out of 2 in 1rgt

Go back to Vanadium Binding Sites List in 1rgt
Vanadium binding site 2 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, 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, Octopamine, and Tetranucleotide Agtc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V699

b:15.0
occ:1.00
V B:VO4699 0.0 15.0 1.0
O1 B:VO4699 1.5 13.8 1.0
O3 B:VO4699 1.5 15.7 1.0
O3' F:DC806 2.0 16.0 1.0
NE2 B:HIS263 2.0 8.6 1.0
O4 B:OTS997 2.1 17.6 0.5
O4 B:OTR998 2.1 17.6 0.5
C3' F:DC806 2.9 13.6 1.0
CE1 B:HIS263 3.0 11.7 1.0
CD2 B:HIS263 3.0 7.0 1.0
C4 B:OTS997 3.1 20.3 0.5
C4 B:OTR998 3.1 20.3 0.5
C3 B:OTS997 3.6 17.6 0.5
C3 B:OTR998 3.6 17.6 0.5
NE2 B:HIS493 3.6 13.5 1.0
CE1 B:HIS493 3.9 12.7 1.0
C2' F:DC806 3.9 15.2 1.0
O B:HOH816 4.0 17.0 1.0
ND1 B:HIS263 4.1 10.1 1.0
C4' F:DC806 4.1 14.9 1.0
ND2 B:ASN516 4.1 9.9 1.0
C5 B:OTS997 4.2 19.1 0.5
C5 B:OTR998 4.2 19.1 0.5
CG B:HIS263 4.2 9.0 1.0
NZ B:LYS265 4.2 11.4 1.0
ND2 B:ASN283 4.2 13.4 1.0
CD2 B:TYR204 4.3 17.5 1.0
CE B:LYS265 4.4 10.2 1.0
NZ B:LYS495 4.4 13.0 1.0
CE B:LYS495 4.7 15.6 1.0
C1' F:DC806 4.7 15.5 1.0
CE2 B:TYR204 4.8 20.0 1.0
CD2 B:HIS493 4.8 11.7 1.0
C2 B:OTS997 4.9 21.8 0.5
C2 B:OTR998 4.9 21.8 0.5

Reference:

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
Page generated: Wed Dec 16 02:30:13 2020

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