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Vanadium in PDB 1rfi: Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Pentapeptide Klnyk, and Tetranucleotide Agtc

Protein crystallography data

The structure of Crystal Structure of Human Tyrosyl-Dna Phosphodiesterase Complexed with Vanadate, Pentapeptide Klnyk, and Tetranucleotide Agtc, PDB code: 1rfi 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.820, 104.832, 193.539, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.7

Vanadium Binding Sites:

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

Vanadium binding site 1 out of 2 in 1rfi

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


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, Pentapeptide Klnyk, and Tetranucleotide Agtc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V699

b:20.1
occ:1.00
V A:VO4699 0.0 20.1 1.0
O1 A:VO4699 1.5 16.7 1.0
O3 A:VO4699 1.5 20.8 1.0
O3' D:DC806 1.8 18.7 1.0
OH C:TYR723 2.0 23.8 1.0
NE2 A:HIS263 2.1 19.0 1.0
C3' D:DC806 2.9 21.3 1.0
CE1 A:HIS263 3.0 15.3 1.0
CZ C:TYR723 3.1 31.2 1.0
CD2 A:HIS263 3.1 18.4 1.0
NE2 A:HIS493 3.5 14.1 1.0
CE2 C:TYR723 3.7 31.3 1.0
C2' D:DC806 3.9 23.6 1.0
O A:HOH752 3.9 22.5 1.0
CE1 A:HIS493 4.0 11.8 1.0
CE1 C:TYR723 4.1 31.9 1.0
C4' D:DC806 4.1 22.3 1.0
ND1 A:HIS263 4.1 17.7 1.0
ND2 A:ASN516 4.2 17.2 1.0
CG A:HIS263 4.2 18.7 1.0
NZ A:LYS265 4.3 15.7 1.0
CD2 A:TYR204 4.3 23.6 1.0
ND2 A:ASN283 4.4 17.2 1.0
NZ A:LYS495 4.4 17.1 1.0
CE A:LYS265 4.5 15.2 1.0
CD2 A:HIS493 4.7 14.4 1.0
C1' D:DC806 4.7 24.6 1.0
CE A:LYS495 4.8 16.2 1.0
CE2 A:TYR204 4.8 24.9 1.0
CD2 C:TYR723 5.0 35.2 1.0
OD1 A:ASN283 5.0 20.2 1.0
O4' D:DC806 5.0 22.6 1.0

Vanadium binding site 2 out of 2 in 1rfi

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


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, Pentapeptide Klnyk, and Tetranucleotide Agtc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V699

b:17.7
occ:1.00
V B:VO4699 0.0 17.7 1.0
O1 B:VO4699 1.5 17.2 1.0
O3 B:VO4699 1.5 15.8 1.0
O3' F:DC806 1.8 16.9 1.0
OH E:TYR723 1.9 25.2 1.0
NE2 B:HIS263 2.0 9.8 1.0
C3' F:DC806 2.9 16.9 1.0
CE1 B:HIS263 2.9 11.7 1.0
CD2 B:HIS263 3.0 14.8 1.0
CZ E:TYR723 3.0 29.0 1.0
CE1 E:TYR723 3.6 31.1 1.0
NE2 B:HIS493 3.7 16.1 1.0
C2' F:DC806 3.7 20.8 1.0
O B:HOH816 3.8 16.3 1.0
CE1 B:HIS493 4.0 16.8 1.0
NZ B:LYS265 4.0 12.5 1.0
C4' F:DC806 4.0 19.6 1.0
CE2 E:TYR723 4.1 29.4 1.0
ND1 B:HIS263 4.1 13.5 1.0
CG B:HIS263 4.1 14.3 1.0
ND2 B:ASN516 4.1 15.3 1.0
CE B:LYS265 4.3 18.0 1.0
CD2 B:TYR204 4.3 20.2 1.0
NZ B:LYS495 4.4 10.9 1.0
ND2 B:ASN283 4.4 13.6 1.0
C1' F:DC806 4.6 21.0 1.0
CE B:LYS495 4.7 12.2 1.0
CE2 B:TYR204 4.8 22.4 1.0
CD2 B:HIS493 4.8 14.8 1.0
O4' F:DC806 4.9 20.7 1.0
CD1 E:TYR723 4.9 31.2 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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