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

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

Protein crystallography data

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

Vanadium Binding Sites:

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 1rgu

Go back to Vanadium Binding Sites List in 1rgu
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 1rgu

Go back to Vanadium Binding Sites List in 1rgu
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

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 7L3L
Zn in 7KSO
Zn in 7KSR
Zn in 7KTP
Zn in 7LMM
Zn in 7LMK
Zn in 7LLZ
Zn in 7LLF
Zn in 7L0N
Zn in 7LBR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy