Fluorine in PDB 4txn: Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil
Enzymatic activity of Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil
All present enzymatic activity of Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil:
2.4.2.3;
Protein crystallography data
The structure of Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil, PDB code: 4txn
was solved by
A.Marinho,
J.Torini,
L.Romanello,
A.Cassago,
R.Demarco,
J.Brandao-Neto,
H.M.Pereira,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.02 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.643,
107.488,
115.576,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
20.7
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil
(pdb code 4txn). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil, PDB code: 4txn:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 4txn
Go back to
Fluorine Binding Sites List in 4txn
Fluorine binding site 1 out
of 4 in the Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F302
b:18.0
occ:1.00
|
F5
|
A:URF302
|
0.0
|
18.0
|
1.0
|
C5
|
A:URF302
|
1.3
|
11.5
|
1.0
|
C4
|
A:URF302
|
2.4
|
15.4
|
1.0
|
C6
|
A:URF302
|
2.4
|
12.0
|
1.0
|
O4
|
A:URF302
|
2.8
|
17.2
|
1.0
|
O
|
A:SER125
|
3.1
|
16.5
|
1.0
|
C
|
A:SER125
|
3.4
|
15.6
|
1.0
|
CD1
|
A:ILE265
|
3.6
|
18.2
|
1.0
|
N1
|
A:URF302
|
3.6
|
15.3
|
1.0
|
N3
|
A:URF302
|
3.6
|
16.8
|
1.0
|
CB
|
A:ALA256
|
3.6
|
16.4
|
1.0
|
N
|
A:GLY126
|
3.7
|
14.2
|
1.0
|
CA
|
A:GLY126
|
4.0
|
18.8
|
1.0
|
C2
|
A:URF302
|
4.0
|
15.0
|
1.0
|
CA
|
A:SER125
|
4.1
|
15.8
|
1.0
|
N
|
A:SER125
|
4.3
|
15.3
|
1.0
|
CG1
|
A:VAL257
|
4.3
|
23.6
|
1.0
|
CE1
|
A:PHE197
|
4.4
|
15.7
|
1.0
|
NH2
|
A:ARG203
|
4.4
|
15.6
|
1.0
|
N
|
A:ALA256
|
4.5
|
18.1
|
1.0
|
CA
|
A:ALA256
|
4.5
|
18.2
|
1.0
|
CG1
|
A:ILE265
|
4.6
|
18.2
|
1.0
|
CZ
|
A:PHE197
|
4.6
|
16.4
|
1.0
|
O
|
A:HOH464
|
4.7
|
29.9
|
1.0
|
C
|
A:ALA256
|
4.9
|
19.2
|
1.0
|
N
|
A:VAL257
|
4.9
|
19.0
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 4txn
Go back to
Fluorine Binding Sites List in 4txn
Fluorine binding site 2 out
of 4 in the Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F302
b:14.3
occ:1.00
|
F5
|
B:URF302
|
0.0
|
14.3
|
1.0
|
C5
|
B:URF302
|
1.3
|
12.9
|
1.0
|
C4
|
B:URF302
|
2.4
|
13.1
|
1.0
|
C6
|
B:URF302
|
2.4
|
14.0
|
1.0
|
O4
|
B:URF302
|
2.8
|
14.4
|
1.0
|
O
|
B:SER125
|
3.2
|
15.1
|
1.0
|
C
|
B:SER125
|
3.4
|
14.9
|
1.0
|
CD1
|
B:ILE265
|
3.5
|
11.3
|
1.0
|
N3
|
B:URF302
|
3.6
|
15.4
|
1.0
|
N1
|
B:URF302
|
3.6
|
14.4
|
1.0
|
N
|
B:GLY126
|
3.7
|
12.0
|
1.0
|
CB
|
B:ALA256
|
3.7
|
17.8
|
1.0
|
CA
|
B:GLY126
|
3.9
|
12.9
|
1.0
|
C2
|
B:URF302
|
4.0
|
14.5
|
1.0
|
CG1
|
B:VAL257
|
4.1
|
11.5
|
1.0
|
NH2
|
B:ARG203
|
4.2
|
14.9
|
1.0
|
CA
|
B:SER125
|
4.2
|
14.3
|
1.0
|
N
|
B:SER125
|
4.3
|
12.8
|
1.0
|
CE1
|
B:PHE197
|
4.4
|
15.8
|
1.0
|
N
|
B:ALA256
|
4.4
|
15.9
|
1.0
|
CG1
|
B:ILE265
|
4.5
|
16.6
|
1.0
|
CA
|
B:ALA256
|
4.5
|
15.8
|
1.0
|
CZ
|
B:PHE197
|
4.5
|
16.1
|
1.0
|
O
|
A:HOH483
|
4.7
|
19.8
|
1.0
|
C
|
B:ALA256
|
4.8
|
14.9
|
1.0
|
N
|
B:VAL257
|
4.9
|
15.5
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 4txn
Go back to
Fluorine Binding Sites List in 4txn
Fluorine binding site 3 out
of 4 in the Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F302
b:16.4
occ:1.00
|
F5
|
C:URF302
|
0.0
|
16.4
|
1.0
|
C5
|
C:URF302
|
1.3
|
15.2
|
1.0
|
C4
|
C:URF302
|
2.4
|
14.9
|
1.0
|
C6
|
C:URF302
|
2.4
|
16.4
|
1.0
|
O4
|
C:URF302
|
2.8
|
14.7
|
1.0
|
O
|
C:SER125
|
3.2
|
16.0
|
1.0
|
C
|
C:SER125
|
3.4
|
15.4
|
1.0
|
CD1
|
C:ILE265
|
3.5
|
19.7
|
1.0
|
N1
|
C:URF302
|
3.6
|
13.8
|
1.0
|
N3
|
C:URF302
|
3.6
|
16.8
|
1.0
|
N
|
C:GLY126
|
3.7
|
15.1
|
1.0
|
CB
|
C:ALA256
|
3.8
|
16.9
|
1.0
|
CA
|
C:GLY126
|
4.0
|
15.4
|
1.0
|
C2
|
C:URF302
|
4.0
|
15.5
|
1.0
|
CA
|
C:SER125
|
4.1
|
16.4
|
1.0
|
CG1
|
C:VAL257
|
4.2
|
13.5
|
1.0
|
N
|
C:SER125
|
4.3
|
14.8
|
1.0
|
NH2
|
C:ARG203
|
4.4
|
14.2
|
1.0
|
CE1
|
C:PHE197
|
4.5
|
15.7
|
1.0
|
N
|
C:ALA256
|
4.5
|
15.1
|
1.0
|
CA
|
C:ALA256
|
4.6
|
17.5
|
1.0
|
CG1
|
C:ILE265
|
4.6
|
20.1
|
1.0
|
CZ
|
C:PHE197
|
4.6
|
14.2
|
1.0
|
C
|
C:ALA256
|
4.9
|
18.0
|
1.0
|
O
|
D:HOH662
|
4.9
|
18.2
|
1.0
|
N
|
C:VAL257
|
5.0
|
15.5
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 4txn
Go back to
Fluorine Binding Sites List in 4txn
Fluorine binding site 4 out
of 4 in the Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Uridine Phosphorylase From Schistosoma Mansoni in Complex with 5-Fluorouracil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F302
b:17.9
occ:1.00
|
F5
|
D:URF302
|
0.0
|
17.9
|
1.0
|
C5
|
D:URF302
|
1.3
|
16.4
|
1.0
|
C4
|
D:URF302
|
2.4
|
16.3
|
1.0
|
C6
|
D:URF302
|
2.4
|
14.5
|
1.0
|
O4
|
D:URF302
|
2.8
|
16.7
|
1.0
|
O
|
D:SER125
|
3.0
|
17.9
|
1.0
|
C
|
D:SER125
|
3.3
|
15.1
|
1.0
|
CB
|
D:ALA256
|
3.6
|
16.7
|
1.0
|
N1
|
D:URF302
|
3.6
|
13.7
|
1.0
|
N3
|
D:URF302
|
3.6
|
15.8
|
1.0
|
CD1
|
D:ILE265
|
3.6
|
18.3
|
1.0
|
N
|
D:GLY126
|
3.7
|
11.6
|
1.0
|
CA
|
D:GLY126
|
4.0
|
16.9
|
1.0
|
C2
|
D:URF302
|
4.0
|
15.8
|
1.0
|
CA
|
D:SER125
|
4.1
|
14.1
|
1.0
|
N
|
D:SER125
|
4.2
|
15.8
|
1.0
|
CG1
|
D:VAL257
|
4.2
|
17.4
|
1.0
|
NH2
|
D:ARG203
|
4.4
|
11.9
|
1.0
|
CE1
|
D:PHE197
|
4.4
|
11.5
|
1.0
|
N
|
D:ALA256
|
4.4
|
11.8
|
1.0
|
CA
|
D:ALA256
|
4.5
|
17.5
|
1.0
|
CG1
|
D:ILE265
|
4.5
|
15.3
|
1.0
|
CZ
|
D:PHE197
|
4.7
|
11.7
|
1.0
|
O
|
D:HOH535
|
4.7
|
18.5
|
1.0
|
C
|
D:ALA256
|
4.8
|
19.8
|
1.0
|
N
|
D:VAL257
|
4.9
|
17.2
|
1.0
|
|
Reference:
A.M.Da Silva Neto,
J.R.Torini De Souza,
L.Romanello,
A.Cassago,
V.H.Serrao,
R.Demarco,
J.Brandao-Neto,
R.C.Garratt,
H.D.Pereira.
Analysis of Two Schistosoma Mansoni Uridine Phosphorylases Isoforms Suggests the Emergence of A Protein with A Non-Canonical Function. Biochimie V. 125 12 2016.
ISSN: ISSN 0300-9084
PubMed: 26898674
DOI: 10.1016/J.BIOCHI.2016.02.007
Page generated: Thu Aug 1 05:45:20 2024
|