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Fluorine in PDB 4e1v: X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution

Enzymatic activity of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution

All present enzymatic activity of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution, PDB code: 4e1v was solved by A.A.Lashkov, S.E.Sotnichenko, I.I.Prokofev, A.G.Gabdoulkhakov, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.88 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.490, 93.210, 149.970, 90.00, 90.82, 90.00
R / Rfree (%) 19.4 / 23.8

Other elements in 4e1v:

The structure of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution also contains other interesting chemical elements:

Potassium (K) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution (pdb code 4e1v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution, PDB code: 4e1v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4e1v

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Fluorine binding site 1 out of 8 in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:43.3
occ:1.00
 F5 A:URF1301 0.0 43.3 1.0
C5 A:URF1301 1.3 42.1 1.0
C6 A:URF1301 2.3 41.9 1.0
C4 A:URF1301 2.4 40.2 1.0
O4 A:URF1301 2.8 39.4 1.0
CG1 A:ILE1220 3.2 35.7 1.0
N A:GLY1096 3.5 32.8 1.0
C A:THR1095 3.5 33.9 1.0
CD1 A:ILE1220 3.5 33.5 1.0
O A:THR1095 3.5 33.2 1.0
CG1 A:VAL1221 3.5 38.0 1.0
N1 A:URF1301 3.7 41.5 1.0
N3 A:URF1301 3.7 39.9 1.0
CA A:GLY1096 3.7 33.7 1.0
CG A:PRO1229 3.8 68.0 1.0
C2 A:URF1301 4.2 40.1 1.0
CA A:THR1095 4.2 34.2 1.0
CB A:VAL1221 4.4 38.8 1.0
N A:THR1095 4.5 35.8 1.0
N A:VAL1221 4.7 39.3 1.0
CB A:ILE1220 4.7 37.9 1.0
NH1 A:ARG1168 4.7 35.5 1.0
CD A:PRO1229 4.8 66.6 1.0
CE2 A:PHE1162 4.9 34.8 1.0
C A:ILE1220 4.9 39.0 1.0
O A:HOH1453 5.0 42.2 1.0

Fluorine binding site 2 out of 8 in 4e1v

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Fluorine binding site 2 out of 8 in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1301

b:32.2
occ:1.00
 F5 E:URF1301 0.0 32.2 1.0
C5 E:URF1301 1.3 28.4 1.0
C6 E:URF1301 2.3 26.7 1.0
C4 E:URF1301 2.4 26.8 1.0
O4 E:URF1301 2.7 31.4 1.0
CG1 E:ILE1220 3.2 43.1 1.0
CD1 E:ILE1220 3.3 42.9 1.0
CG1 E:VAL1221 3.4 39.6 1.0
N E:GLY1096 3.5 31.3 1.0
C E:THR1095 3.5 33.0 1.0
O E:THR1095 3.6 33.4 1.0
CG E:PRO1229 3.6 58.5 1.0
N1 E:URF1301 3.7 26.3 1.0
N3 E:URF1301 3.7 25.4 1.0
CA E:GLY1096 3.7 31.6 1.0
C2 E:URF1301 4.2 25.9 1.0
CA E:THR1095 4.3 33.3 1.0
N E:THR1095 4.4 34.0 1.0
CB E:VAL1221 4.5 44.4 1.0
CD E:PRO1229 4.6 58.9 1.0
N E:VAL1221 4.7 41.0 1.0
NH1 E:ARG1168 4.7 33.2 1.0
CB E:ILE1220 4.7 43.9 1.0
CB E:PRO1229 4.7 60.4 1.0
CE2 E:PHE1162 4.8 28.3 1.0
OG1 E:THR1094 5.0 39.8 1.0

Fluorine binding site 3 out of 8 in 4e1v

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Fluorine binding site 3 out of 8 in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1301

b:47.6
occ:1.00
 F5 F:URF1301 0.0 47.6 1.0
C5 F:URF1301 1.3 46.3 1.0
C6 F:URF1301 2.3 45.6 1.0
C4 F:URF1301 2.4 45.4 1.0
O4 F:URF1301 2.8 45.4 1.0
CG1 F:ILE1220 3.3 38.7 1.0
CD1 F:ILE1220 3.3 38.6 1.0
C F:THR1095 3.6 41.5 1.0
N F:GLY1096 3.6 40.1 1.0
CG1 F:VAL1221 3.6 37.9 1.0
N1 F:URF1301 3.6 44.8 1.0
O F:THR1095 3.6 40.6 1.0
N3 F:URF1301 3.7 43.7 1.0
CA F:GLY1096 3.9 38.9 1.0
C2 F:URF1301 4.2 44.1 1.0
CA F:THR1095 4.2 42.1 1.0
N F:THR1095 4.5 43.1 1.0
NH2 F:ARG1168 4.6 33.8 1.0
CG F:PRO1229 4.6 56.1 1.0
CB F:VAL1221 4.6 40.2 1.0
CE2 F:PHE1162 4.7 37.0 1.0
CB F:ILE1220 4.8 40.9 1.0
N F:VAL1221 4.8 40.5 1.0
CD F:PRO1229 4.9 55.7 1.0

Fluorine binding site 4 out of 8 in 4e1v

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Fluorine binding site 4 out of 8 in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1301

b:38.1
occ:1.00
 F5 D:URF1301 0.0 38.1 1.0
C5 D:URF1301 1.3 35.0 1.0
C6 D:URF1301 2.3 33.3 1.0
C4 D:URF1301 2.4 34.0 1.0
O4 D:URF1301 2.7 32.9 1.0
CG1 D:ILE1220 3.2 43.1 1.0
N D:GLY1096 3.4 34.2 1.0
CG1 D:VAL1221 3.4 40.7 1.0
CD1 D:ILE1220 3.4 42.5 1.0
C D:THR1095 3.4 36.4 1.0
O D:THR1095 3.6 35.0 1.0
N1 D:URF1301 3.6 33.5 1.0
N3 D:URF1301 3.7 34.3 1.0
CG D:PRO1229 3.7 51.3 1.0
CA D:GLY1096 3.7 34.1 1.0
C2 D:URF1301 4.2 33.8 1.0
CA D:THR1095 4.2 37.8 1.0
CB D:VAL1221 4.4 41.5 1.0
N D:THR1095 4.4 39.9 1.0
CB D:ILE1220 4.7 42.4 1.0
CB D:PRO1229 4.7 52.3 1.0
N D:VAL1221 4.7 40.1 1.0
NH2 D:ARG1168 4.7 32.9 1.0
CD D:PRO1229 4.8 52.0 1.0
CE2 D:PHE1162 4.9 33.7 1.0
C D:ILE1220 4.9 41.6 1.0

Fluorine binding site 5 out of 8 in 4e1v

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Fluorine binding site 5 out of 8 in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1301

b:41.3
occ:1.00
 F5 C:URF1301 0.0 41.3 1.0
C5 C:URF1301 1.3 38.5 1.0
C6 C:URF1301 2.3 38.2 1.0
C4 C:URF1301 2.4 35.8 1.0
O4 C:URF1301 2.8 33.5 1.0
CG1 C:VAL1221 3.2 38.2 1.0
CG1 C:ILE1220 3.2 41.9 1.0
N C:GLY1096 3.4 35.8 1.0
CD1 C:ILE1220 3.4 41.2 1.0
C C:THR1095 3.4 38.9 1.0
O C:THR1095 3.5 39.3 1.0
CA C:GLY1096 3.6 36.3 1.0
N1 C:URF1301 3.7 39.5 1.0
N3 C:URF1301 3.7 35.6 1.0
CG C:PRO1229 3.8 51.9 1.0
C2 C:URF1301 4.2 37.8 1.0
CA C:THR1095 4.2 41.0 1.0
CB C:VAL1221 4.4 40.0 1.0
N C:THR1095 4.5 41.5 1.0
N C:VAL1221 4.5 39.8 1.0
CB C:ILE1220 4.7 42.5 1.0
CB C:PRO1229 4.7 54.3 1.0
NH1 C:ARG1168 4.8 32.0 1.0
CD C:PRO1229 4.8 51.5 1.0
C C:ILE1220 4.9 41.7 1.0
CE2 C:PHE1162 5.0 28.1 1.0

Fluorine binding site 6 out of 8 in 4e1v

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Fluorine binding site 6 out of 8 in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1301

b:37.9
occ:1.00
 F5 B:URF1301 0.0 37.9 1.0
C5 B:URF1301 1.3 34.4 1.0
C6 B:URF1301 2.3 31.9 1.0
C4 B:URF1301 2.4 34.3 1.0
O4 B:URF1301 2.8 36.6 1.0
CG1 B:ILE1220 3.2 36.7 1.0
CD1 B:ILE1220 3.2 36.5 1.0
CG1 B:VAL1221 3.3 47.5 1.0
O B:THR1095 3.5 35.2 1.0
C B:THR1095 3.5 35.5 1.0
N B:GLY1096 3.6 34.2 1.0
CG B:PRO1229 3.6 54.9 1.0
N1 B:URF1301 3.6 30.6 1.0
N3 B:URF1301 3.7 32.1 1.0
CA B:GLY1096 3.8 34.2 1.0
C2 B:URF1301 4.2 30.8 1.0
CA B:THR1095 4.3 36.4 1.0
CB B:VAL1221 4.4 49.0 1.0
N B:THR1095 4.6 37.0 1.0
N B:VAL1221 4.6 40.4 1.0
CD B:PRO1229 4.6 55.8 1.0
CB B:ILE1220 4.6 39.0 1.0
NH1 B:ARG1168 4.7 33.1 1.0
CB B:PRO1229 4.7 57.0 1.0
CE2 B:PHE1162 4.9 32.2 1.0
C B:ILE1220 5.0 40.1 1.0

Fluorine binding site 7 out of 8 in 4e1v

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Fluorine binding site 7 out of 8 in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F1301

b:72.9
occ:1.00
 F5 H:URF1301 0.0 72.9 1.0
C5 H:URF1301 1.3 73.0 1.0
C6 H:URF1301 2.3 73.0 1.0
C4 H:URF1301 2.4 73.6 1.0
O4 H:URF1301 2.8 73.9 1.0
CG1 H:VAL1221 3.2 65.9 1.0
CG1 H:ILE1220 3.3 66.0 1.0
C H:THR1095 3.4 65.0 1.0
N H:GLY1096 3.4 64.0 1.0
CD1 H:ILE1220 3.4 66.3 1.0
O H:THR1095 3.5 65.1 1.0
N1 H:URF1301 3.7 72.5 1.0
CA H:GLY1096 3.7 63.5 1.0
N3 H:URF1301 3.7 73.6 1.0
CG H:PRO1229 3.9 85.1 1.0
CA H:THR1095 4.2 66.0 1.0
C2 H:URF1301 4.2 72.2 1.0
CB H:VAL1221 4.5 66.7 1.0
N H:THR1095 4.5 67.3 1.0
NH2 H:ARG1168 4.7 59.8 1.0
CE2 H:PHE1162 4.8 58.7 1.0
N H:VAL1221 4.8 66.9 1.0
CB H:ILE1220 4.8 67.5 1.0
CD H:PRO1229 4.8 84.0 1.0
CB H:PRO1229 4.9 87.2 1.0

Fluorine binding site 8 out of 8 in 4e1v

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Fluorine binding site 8 out of 8 in the X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of X-Ray Structure of the Uridine Phosphorylase From Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F1301

b:72.8
occ:1.00
 F5 G:URF1301 0.0 72.8 1.0
C5 G:URF1301 1.3 73.5 1.0
C6 G:URF1301 2.3 73.7 1.0
C4 G:URF1301 2.4 73.7 1.0
O4 G:URF1301 2.8 73.5 1.0
CG1 G:ILE1220 3.4 85.9 1.0
CD1 G:ILE1220 3.4 85.4 1.0
CG G:PRO1229 3.6 94.6 1.0
CG1 G:VAL1221 3.6 79.2 1.0
O G:THR1095 3.6 85.3 1.0
N1 G:URF1301 3.7 73.9 1.0
N3 G:URF1301 3.7 73.8 1.0
C G:THR1095 3.7 84.5 1.0
N G:GLY1096 4.0 82.2 1.0
C2 G:URF1301 4.2 73.5 1.0
CA G:GLY1096 4.3 82.2 1.0
CA G:THR1095 4.3 86.1 1.0
NH2 G:ARG1168 4.4 70.8 1.0
CB G:VAL1221 4.5 81.6 1.0
CE2 G:PHE1162 4.5 73.4 1.0
N G:THR1095 4.5 87.2 1.0
CB G:PRO1229 4.6 97.2 1.0
CD G:PRO1229 4.7 93.5 1.0
CZ G:PHE1162 4.8 73.8 1.0
CB G:ILE1220 4.9 88.2 1.0

Reference:

A.A.Lashkov, S.E.Sotnichenko, I.I.Prokofiev, A.G.Gabdulkhakov, I.I.Agapov, A.A.Shtil, C.Betzel, A.S.Mironov, A.M.Mikhailov. X-Ray Structure of Salmonella Typhimurium Uridine Phosphorylase Complexed with 5-Fluorouracil and Molecular Modelling of the Complex of 5-Fluorouracil with Uridine Phosphorylase From Vibrio Cholerae. Acta Crystallogr.,Sect.D V. 68 968 2012.
ISSN: ISSN 0907-4449
PubMed: 22868762
DOI: 10.1107/S090744491201815X
Page generated: Thu Aug 1 01:10:15 2024

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