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Vanadium in PDB 1rg2: Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agta

Protein crystallography data

The structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agta, PDB code: 1rg2 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.811, 104.688, 193.310, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.3

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agta (pdb code 1rg2). 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 Agta, PDB code: 1rg2:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 1rg2

Go back to Vanadium Binding Sites List in 1rg2
Vanadium binding site 1 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agta


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

b:16.0
occ:1.00
V A:VO4699 0.0 16.0 1.0
O1 A:VO4699 1.5 10.5 1.0
O3 A:VO4699 1.5 15.7 1.0
O3' D:DA806 1.8 14.0 1.0
O4 A:OTS995 1.9 18.4 0.5
O4 A:OTR996 1.9 18.4 0.5
NE2 A:HIS263 2.0 11.9 1.0
C3' D:DA806 2.9 19.0 1.0
CE1 A:HIS263 2.9 10.6 1.0
C4 A:OTS995 3.0 20.2 0.5
C4 A:OTR996 3.0 20.2 0.5
CD2 A:HIS263 3.0 9.6 1.0
C3 A:OTS995 3.4 20.0 0.5
C3 A:OTR996 3.4 20.0 0.5
NE2 A:HIS493 3.5 12.1 1.0
C2' D:DA806 3.8 18.6 1.0
CE1 A:HIS493 3.8 12.5 1.0
O A:HOH706 3.9 16.8 1.0
C4' D:DA806 4.0 19.7 1.0
ND1 A:HIS263 4.1 11.8 1.0
ND2 A:ASN516 4.1 10.6 1.0
C5 A:OTS995 4.1 18.9 0.5
C5 A:OTR996 4.1 18.9 0.5
CG A:HIS263 4.1 12.7 1.0
NZ A:LYS265 4.4 13.9 1.0
ND2 A:ASN283 4.4 9.6 1.0
CD2 A:TYR204 4.4 20.6 1.0
CE A:LYS265 4.4 14.1 1.0
NZ A:LYS495 4.4 11.9 1.0
CD2 A:HIS493 4.7 11.7 1.0
C1' D:DA806 4.7 21.1 1.0
CE A:LYS495 4.8 12.2 1.0
C2 A:OTS995 4.8 21.3 0.5
C2 A:OTR996 4.8 21.3 0.5
CE2 A:TYR204 4.8 21.6 1.0
O4' D:DA806 4.9 19.8 1.0

Vanadium binding site 2 out of 2 in 1rg2

Go back to Vanadium Binding Sites List in 1rg2
Vanadium binding site 2 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octopamine, and Tetranucleotide Agta


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

b:16.4
occ:1.00
V B:VO4699 0.0 16.4 1.0
O1 B:VO4699 1.5 17.8 1.0
O3 B:VO4699 1.5 16.9 1.0
O3' F:DA806 1.8 16.2 1.0
NE2 B:HIS263 2.0 9.2 1.0
O4 B:OTS997 2.1 19.0 0.5
O4 B:OTR998 2.1 19.0 0.5
C3' F:DA806 2.9 17.4 1.0
CE1 B:HIS263 3.0 12.1 1.0
CD2 B:HIS263 3.0 10.5 1.0
C4 B:OTS997 3.1 21.7 0.5
C4 B:OTR998 3.1 21.7 0.5
NE2 B:HIS493 3.6 14.7 1.0
C3 B:OTS997 3.6 21.0 0.5
C3 B:OTR998 3.6 21.0 0.5
C2' F:DA806 3.8 17.2 1.0
O B:HOH676 3.9 12.0 1.0
CE1 B:HIS493 4.0 13.5 1.0
NZ B:LYS265 4.0 11.2 1.0
ND2 B:ASN516 4.1 9.0 1.0
C4' F:DA806 4.1 17.9 1.0
ND1 B:HIS263 4.1 11.2 1.0
CG B:HIS263 4.2 12.3 1.0
C5 B:OTS997 4.3 19.3 0.5
C5 B:OTR998 4.3 19.3 0.5
ND2 B:ASN283 4.3 11.0 1.0
CE B:LYS265 4.3 11.9 1.0
CD2 B:TYR204 4.4 21.1 1.0
NZ B:LYS495 4.5 10.1 1.0
CE B:LYS495 4.6 11.9 1.0
CD2 B:HIS493 4.7 10.3 1.0
C1' F:DA806 4.7 21.0 1.0
CE2 B:TYR204 4.9 19.4 1.0
C2 B:OTS997 4.9 21.7 0.5
C2 B:OTR998 4.9 21.7 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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