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Vanadium in PDB 1rff: Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octapeptide Klnyydpr, and Tetranucleotide Agtt.

Protein crystallography data

The structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octapeptide Klnyydpr, and Tetranucleotide Agtt., PDB code: 1rff 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.076, 104.904, 193.832, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 21.3

Vanadium Binding Sites:

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

Vanadium binding site 1 out of 2 in 1rff

Go back to Vanadium Binding Sites List in 1rff
Vanadium binding site 1 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octapeptide Klnyydpr, and Tetranucleotide Agtt.


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, Octapeptide Klnyydpr, and Tetranucleotide Agtt. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V699

b:15.7
occ:1.00
V A:VO4699 0.0 15.7 1.0
O3 A:VO4699 1.5 16.1 1.0
O1 A:VO4699 1.6 18.3 1.0
O3' D:DT806 1.8 17.3 1.0
OH C:TYR723 2.0 20.4 1.0
NE2 A:HIS263 2.1 15.3 1.0
C3' D:DT806 2.9 17.1 1.0
CZ C:TYR723 3.1 15.6 1.0
CE1 A:HIS263 3.1 13.7 1.0
CD2 A:HIS263 3.1 15.9 1.0
NE2 A:HIS493 3.5 13.0 1.0
CE2 C:TYR723 3.6 17.1 1.0
C2' D:DT806 3.8 17.5 1.0
CE1 A:HIS493 3.8 13.3 1.0
O A:HOH730 3.9 17.2 1.0
C4' D:DT806 4.1 18.7 1.0
CE1 C:TYR723 4.1 14.0 1.0
ND2 A:ASN516 4.2 15.0 1.0
NZ A:LYS265 4.2 14.7 1.0
ND1 A:HIS263 4.2 15.1 1.0
ND2 A:ASN283 4.3 15.1 1.0
CG A:HIS263 4.3 15.5 1.0
CD2 A:TYR204 4.3 18.9 1.0
NZ A:LYS495 4.3 17.4 1.0
CE A:LYS265 4.4 18.3 1.0
C1' D:DT806 4.6 16.2 1.0
CD2 A:HIS493 4.7 16.2 1.0
CE A:LYS495 4.7 15.2 1.0
CE2 A:TYR204 4.8 21.7 1.0
CD2 C:TYR723 4.9 15.6 1.0
O4' D:DT806 4.9 17.0 1.0
OD1 A:ASN283 5.0 16.9 1.0

Vanadium binding site 2 out of 2 in 1rff

Go back to Vanadium Binding Sites List in 1rff
Vanadium binding site 2 out of 2 in the Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Octapeptide Klnyydpr, and Tetranucleotide Agtt.


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, Octapeptide Klnyydpr, and Tetranucleotide Agtt. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V699

b:13.7
occ:1.00
V B:VO4699 0.0 13.7 1.0
O1 B:VO4699 1.5 17.4 1.0
O3 B:VO4699 1.5 16.3 1.0
O3' F:DT806 1.9 15.6 1.0
OH E:TYR723 2.0 14.6 1.0
NE2 B:HIS263 2.1 13.0 1.0
C3' F:DT806 2.8 12.6 1.0
CE1 B:HIS263 3.0 13.9 1.0
CZ E:TYR723 3.1 12.8 1.0
CD2 B:HIS263 3.2 11.6 1.0
NE2 B:HIS493 3.5 13.1 1.0
CE1 E:TYR723 3.5 14.4 1.0
C2' F:DT806 3.8 14.2 1.0
CE1 B:HIS493 3.9 14.8 1.0
O B:HOH676 3.9 18.7 1.0
C4' F:DT806 4.0 16.2 1.0
NZ B:LYS265 4.1 16.1 1.0
CE2 E:TYR723 4.1 14.8 1.0
ND2 B:ASN516 4.2 12.6 1.0
ND1 B:HIS263 4.2 14.2 1.0
ND2 B:ASN283 4.2 15.3 1.0
CG B:HIS263 4.3 13.1 1.0
CD2 B:TYR204 4.3 19.5 1.0
CE B:LYS265 4.3 15.6 1.0
NZ B:LYS495 4.4 12.7 1.0
C1' F:DT806 4.5 16.4 1.0
CE B:LYS495 4.6 13.9 1.0
CD2 B:HIS493 4.7 11.6 1.0
CE2 B:TYR204 4.8 19.5 1.0
O4' F:DT806 4.9 18.5 1.0
CD1 E:TYR723 4.9 17.7 1.0
OD1 B:ASN283 5.0 15.3 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: Thu Oct 29 07:04:22 2020

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