Atomistry » Vanadium » PDB 1b8j-1yv3 » 1rh0
Atomistry »
  Vanadium »
    PDB 1b8j-1yv3 »
      1rh0 »

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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy