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Fluorine in PDB 1upf: Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil

Enzymatic activity of Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil

All present enzymatic activity of Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil:
2.4.2.9;

Protein crystallography data

The structure of Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil, PDB code: 1upf was solved by M.A.Schumacher, D.Carter, D.Scott, D.Roos, B.Ullman, R.G.Brennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.460, 141.780, 71.460, 90.00, 115.03, 90.00
R / Rfree (%) n/a / n/a

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil (pdb code 1upf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil, PDB code: 1upf:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1upf

Go back to Fluorine Binding Sites List in 1upf
Fluorine binding site 1 out of 4 in the Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F999

b:58.8
occ:1.00
 F5 D:URF999 0.0 58.8 1.0
C5 D:URF999 1.3 38.2 1.0
C6 D:URF999 2.3 43.0 1.0
C4 D:URF999 2.4 28.2 1.0
O4 D:URF999 2.8 41.2 1.0
CD1 D:ILE229 3.0 17.6 1.0
N D:ILE229 3.0 20.5 1.0
CB D:ALA168 3.0 25.9 1.0
O D:TYR227 3.1 47.4 1.0
CA D:TYR228 3.4 34.9 1.0
C D:TYR228 3.5 27.6 1.0
N3 D:URF999 3.6 43.1 1.0
N1 D:URF999 3.6 64.4 1.0
CG1 D:ILE229 3.7 25.8 1.0
CA D:ALA168 3.8 25.7 1.0
C D:TYR227 3.8 48.8 1.0
N D:TYR228 4.0 41.4 1.0
CA D:ILE229 4.0 19.4 1.0
CD1 D:LEU223 4.1 43.4 1.0
C2 D:URF999 4.1 59.0 1.0
CB D:ILE229 4.2 22.3 1.0
N D:ALA168 4.2 24.4 1.0
CD1 D:TYR228 4.6 46.5 1.0
O D:TYR228 4.6 25.4 1.0
CB D:TYR228 4.7 37.5 1.0

Fluorine binding site 2 out of 4 in 1upf

Go back to Fluorine Binding Sites List in 1upf
Fluorine binding site 2 out of 4 in the Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F999

b:55.8
occ:1.00
 F5 C:URF999 0.0 55.8 1.0
C5 C:URF999 1.3 59.8 1.0
C6 C:URF999 2.3 35.9 1.0
C4 C:URF999 2.4 25.6 1.0
O4 C:URF999 2.8 23.1 1.0
CB C:ALA168 3.0 24.8 1.0
O C:TYR227 3.1 36.5 1.0
CG1 C:ILE229 3.4 25.6 1.0
N1 C:URF999 3.6 65.1 1.0
N3 C:URF999 3.6 52.1 1.0
CD1 C:ILE229 3.6 27.1 1.0
N C:ILE229 3.6 31.7 1.0
CA C:TYR228 3.8 33.8 1.0
O C:HOH1032 3.9 52.6 1.0
CA C:ALA168 4.0 25.4 1.0
C C:TYR228 4.1 32.5 1.0
C2 C:URF999 4.1 67.0 1.0
C C:TYR227 4.1 40.1 1.0
CD2 C:LEU223 4.3 34.3 1.0
N C:ALA168 4.4 23.5 1.0
CB C:ILE229 4.4 25.4 1.0
N C:TYR228 4.5 33.4 1.0
CA C:ILE229 4.6 27.0 1.0
CD2 C:TYR228 4.9 65.6 1.0
CG C:TYR228 4.9 58.9 1.0
CB C:TYR228 4.9 41.2 1.0

Fluorine binding site 3 out of 4 in 1upf

Go back to Fluorine Binding Sites List in 1upf
Fluorine binding site 3 out of 4 in the Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F999

b:59.1
occ:1.00
 F5 B:URF999 0.0 59.1 1.0
C5 B:URF999 1.3 92.4 1.0
C6 B:URF999 2.3 61.9 1.0
C4 B:URF999 2.4 35.4 1.0
O4 B:URF999 2.8 43.8 1.0
O B:TYR227 2.8 39.6 1.0
CA B:TYR228 3.2 26.6 1.0
N B:ILE229 3.2 25.3 1.0
CG1 B:ILE229 3.4 26.4 1.0
N3 B:URF999 3.6 59.3 1.0
C B:TYR228 3.6 30.3 1.0
N1 B:URF999 3.6 61.3 1.0
CD1 B:TYR228 3.7 42.0 1.0
CB B:ALA168 3.7 24.9 1.0
C B:TYR227 3.7 37.9 1.0
O B:HOH1036 3.9 94.0 1.0
N B:TYR228 3.9 30.4 1.0
C2 B:URF999 4.1 48.3 1.0
CB B:TYR228 4.2 27.7 1.0
CG B:TYR228 4.2 33.4 1.0
CD1 B:ILE229 4.2 11.5 1.0
CB B:ILE229 4.2 26.8 1.0
CA B:ILE229 4.3 22.5 1.0
CE1 B:TYR228 4.4 46.1 1.0
O B:TYR228 4.7 32.0 1.0
O B:HOH1002 4.7 29.3 1.0
CA B:ALA168 4.8 22.6 1.0

Fluorine binding site 4 out of 4 in 1upf

Go back to Fluorine Binding Sites List in 1upf
Fluorine binding site 4 out of 4 in the Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Uracil Phosphoribosyltransferase, Mutant C128V Bound to the Drug 5-Fluorouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:72.5
occ:1.00
 F5 A:URF999 0.0 72.5 1.0
C5 A:URF999 1.3 25.0 1.0
C6 A:URF999 2.3 54.9 1.0
C4 A:URF999 2.4 69.3 1.0
O4 A:URF999 2.8 43.3 1.0
O A:TYR227 3.0 34.6 1.0
CB A:ALA168 3.1 19.1 1.0
N1 A:URF999 3.6 43.7 1.0
N3 A:URF999 3.6 50.1 1.0
CA A:TYR228 3.7 37.9 1.0
N A:ILE229 3.7 26.3 1.0
CG1 A:ILE229 3.8 20.2 1.0
C A:TYR227 4.0 33.0 1.0
C2 A:URF999 4.1 54.0 1.0
CD1 A:ILE229 4.1 34.6 1.0
C A:TYR228 4.2 33.7 1.0
N A:TYR228 4.3 33.4 1.0
CA A:ALA168 4.4 20.1 1.0
CD2 A:TYR228 4.5 66.8 1.0
CG A:TYR228 4.6 62.0 1.0
CB A:ILE229 4.7 23.4 1.0
CB A:TYR228 4.7 47.5 1.0
CA A:ILE229 4.8 23.3 1.0
N A:ALA168 4.8 18.1 1.0
CE2 A:TYR228 5.0 72.2 1.0

Reference:

M.A.Schumacher, D.Carter, D.M.Scott, D.S.Roos, B.Ullman, R.G.Brennan. Crystal Structures of Toxoplasma Gondii Uracil Phosphoribosyltransferase Reveal the Atomic Basis of Pyrimidine Discrimination and Prodrug Binding. Embo J. V. 17 3219 1998.
ISSN: ISSN 0261-4189
PubMed: 9628859
DOI: 10.1093/EMBOJ/17.12.3219
Page generated: Mon Jul 14 12:03:14 2025

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