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Vanadium in PDB 1rh0: Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine and Trinucleotide Gtt

Protein crystallography data

The structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine and Trinucleotide Gtt, PDB code: 1rh0 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 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.692, 104.750, 194.033, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.5

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine and Trinucleotide Gtt (pdb code 1rh0). 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 Trinucleotide Gtt, PDB code: 1rh0:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 1rh0

Go back to Vanadium Binding Sites List in 1rh0
Vanadium binding site 1 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine and Trinucleotide Gtt


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 Trinucleotide Gtt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V699

b:23.6
occ:1.00
V A:VO4699 0.0 23.6 1.0
O3 A:VO4699 1.5 21.4 1.0
O1 A:VO4699 1.5 18.1 1.0
O3' D:DT806 1.9 25.3 1.0
O4 A:OTS995 2.0 23.6 1.0
NE2 A:HIS263 2.1 22.4 1.0
C3' D:DT806 3.0 32.9 1.0
CE1 A:HIS263 3.1 21.1 1.0
C4 A:OTS995 3.1 27.0 1.0
CD2 A:HIS263 3.2 20.4 1.0
NE2 A:HIS493 3.4 18.5 1.0
C3 A:OTS995 3.4 26.5 1.0
O A:HOH706 3.7 22.8 1.0
C2' D:DT806 3.9 34.0 1.0
CE1 A:HIS493 3.9 14.6 1.0
C4' D:DT806 4.1 33.3 1.0
ND2 A:ASN516 4.2 20.3 1.0
ND1 A:HIS263 4.2 20.9 1.0
C5 A:OTS995 4.3 27.5 1.0
CG A:HIS263 4.3 21.4 1.0
ND2 A:ASN283 4.3 22.2 1.0
NZ A:LYS495 4.4 17.9 1.0
NZ A:LYS265 4.4 16.4 1.0
CE A:LYS265 4.5 15.3 1.0
CD2 A:HIS493 4.5 13.6 1.0
CD2 A:TYR204 4.5 27.2 1.0
CE A:LYS495 4.7 20.2 1.0
C1' D:DT806 4.7 34.6 1.0
C2 A:OTS995 4.8 29.0 1.0
CE2 A:TYR204 5.0 29.6 1.0

Vanadium binding site 2 out of 2 in 1rh0

Go back to Vanadium Binding Sites List in 1rh0
Vanadium binding site 2 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine and Trinucleotide Gtt


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 Trinucleotide Gtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V699

b:24.2
occ:1.00
V B:VO4699 0.0 24.2 1.0
O1 B:VO4699 1.5 16.9 1.0
O3 B:VO4699 1.5 18.3 1.0
O3' F:DT806 1.8 20.0 1.0
O4 B:OTS996 2.0 25.7 1.0
NE2 B:HIS263 2.1 12.6 1.0
C3' F:DT806 2.8 26.6 1.0
C4 B:OTS996 3.0 26.8 1.0
CE1 B:HIS263 3.0 10.9 1.0
CD2 B:HIS263 3.1 12.4 1.0
C3 B:OTS996 3.4 28.5 1.0
NE2 B:HIS493 3.6 16.9 1.0
C2' F:DT806 3.7 26.5 1.0
O B:HOH676 3.9 22.8 1.0
CE1 B:HIS493 4.0 17.6 1.0
C4' F:DT806 4.0 27.8 1.0
NZ B:LYS265 4.1 11.7 1.0
ND1 B:HIS263 4.2 12.6 1.0
C5 B:OTS996 4.2 27.3 1.0
CG B:HIS263 4.2 13.1 1.0
ND2 B:ASN516 4.2 17.5 1.0
CE B:LYS265 4.3 13.8 1.0
ND2 B:ASN283 4.4 11.2 1.0
NZ B:LYS495 4.5 14.2 1.0
CD2 B:TYR204 4.5 22.1 1.0
C1' F:DT806 4.5 30.3 1.0
CE B:LYS495 4.6 13.8 1.0
C2 B:OTS996 4.7 31.3 1.0
CD2 B:HIS493 4.8 15.3 1.0
O4' F:DT806 4.8 30.5 1.0
CE2 B:TYR204 5.0 26.6 1.0

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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