Fluorine in PDB 4fog: Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid
Enzymatic activity of Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid
All present enzymatic activity of Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid:
2.1.1.45;
Protein crystallography data
The structure of Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid, PDB code: 4fog
was solved by
M.C.M.Reddy,
J.B.Bruning,
W.Harshbarger,
J.C.Sacchettini,
Tb Structuralgenomics Consortium (Tbsgc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.94 /
2.40
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
184.328,
82.317,
125.980,
90.00,
132.30,
90.00
|
R / Rfree (%)
|
21.1 /
26
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid
(pdb code 4fog). 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 Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid, PDB code: 4fog:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 4fog
Go back to
Fluorine Binding Sites List in 4fog
Fluorine binding site 1 out
of 4 in the Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid
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 Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:60.8
occ:1.00
|
F5
|
A:UFP301
|
0.0
|
60.8
|
1.0
|
C5
|
A:UFP301
|
1.4
|
58.2
|
1.0
|
C6
|
A:UFP301
|
2.4
|
57.5
|
1.0
|
C4
|
A:UFP301
|
2.4
|
53.5
|
1.0
|
N5
|
A:C2F302
|
2.7
|
63.6
|
1.0
|
C11
|
A:C2F302
|
2.9
|
64.6
|
1.0
|
O4
|
A:UFP301
|
3.0
|
56.0
|
1.0
|
C6
|
A:C2F302
|
3.2
|
60.2
|
1.0
|
OH
|
A:TYR94
|
3.4
|
39.2
|
1.0
|
O
|
A:HOH429
|
3.6
|
44.7
|
1.0
|
C4A
|
A:C2F302
|
3.6
|
58.8
|
1.0
|
N1
|
A:UFP301
|
3.7
|
54.1
|
1.0
|
N3
|
A:UFP301
|
3.7
|
47.5
|
1.0
|
SG
|
A:CYS146
|
3.7
|
47.0
|
0.7
|
C7
|
A:C2F302
|
3.7
|
55.6
|
1.0
|
CB
|
A:CYS146
|
4.1
|
41.0
|
0.3
|
CB
|
A:CYS146
|
4.1
|
40.7
|
0.7
|
C2
|
A:UFP301
|
4.2
|
50.8
|
1.0
|
CZ2
|
A:TRP80
|
4.3
|
47.8
|
1.0
|
CH2
|
A:TRP80
|
4.3
|
43.6
|
1.0
|
CZ
|
A:TYR94
|
4.4
|
36.3
|
1.0
|
N8
|
A:C2F302
|
4.4
|
53.9
|
1.0
|
C8A
|
A:C2F302
|
4.4
|
55.2
|
1.0
|
C4
|
A:C2F302
|
4.5
|
56.4
|
1.0
|
C9
|
A:C2F302
|
4.5
|
61.4
|
1.0
|
O4
|
A:C2F302
|
4.6
|
58.4
|
1.0
|
CE2
|
A:TYR94
|
4.6
|
37.0
|
1.0
|
O4'
|
A:UFP301
|
4.6
|
57.1
|
1.0
|
N10
|
A:C2F302
|
4.7
|
60.0
|
1.0
|
C1'
|
A:UFP301
|
4.8
|
56.5
|
1.0
|
SG
|
A:CYS146
|
4.9
|
42.3
|
0.3
|
ND1
|
A:HIS147
|
5.0
|
38.9
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 4fog
Go back to
Fluorine Binding Sites List in 4fog
Fluorine binding site 2 out
of 4 in the Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid
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 Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:48.3
occ:0.57
|
F5
|
B:UFP301
|
0.0
|
48.3
|
0.6
|
C5
|
B:UFP301
|
1.4
|
45.2
|
0.6
|
C4
|
B:UFP301
|
2.4
|
37.2
|
0.6
|
C6
|
B:UFP301
|
2.4
|
46.8
|
0.6
|
O4
|
B:UFP301
|
2.7
|
38.5
|
0.6
|
O
|
B:HOH440
|
3.0
|
45.6
|
1.0
|
OH
|
B:TYR94
|
3.4
|
34.5
|
1.0
|
N1
|
B:UFP301
|
3.6
|
46.1
|
0.6
|
N3
|
B:UFP301
|
3.7
|
39.7
|
0.6
|
O
|
B:HOH438
|
3.9
|
48.8
|
1.0
|
CD2
|
B:HIS147
|
3.9
|
34.2
|
1.0
|
CB
|
B:CYS146
|
4.0
|
40.0
|
1.0
|
NE2
|
B:HIS147
|
4.1
|
30.9
|
1.0
|
SG
|
B:CYS146
|
4.1
|
46.5
|
1.0
|
O
|
B:HOH476
|
4.2
|
48.8
|
1.0
|
C2
|
B:UFP301
|
4.2
|
36.9
|
0.6
|
CZ
|
B:TYR94
|
4.3
|
37.9
|
1.0
|
CE2
|
B:TYR94
|
4.5
|
38.9
|
1.0
|
O4'
|
B:UFP301
|
4.7
|
47.2
|
0.6
|
C1'
|
B:UFP301
|
4.7
|
43.5
|
0.6
|
CZ2
|
B:TRP80
|
4.8
|
47.8
|
1.0
|
OD1
|
B:ASN177
|
5.0
|
35.1
|
1.0
|
N
|
B:CYS146
|
5.0
|
41.5
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 4fog
Go back to
Fluorine Binding Sites List in 4fog
Fluorine binding site 3 out
of 4 in the Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid
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 Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F301
b:53.8
occ:1.00
|
F5
|
C:UFP301
|
0.0
|
53.8
|
1.0
|
C5
|
C:UFP301
|
1.4
|
54.2
|
1.0
|
C6
|
C:UFP301
|
2.4
|
52.8
|
1.0
|
C4
|
C:UFP301
|
2.5
|
45.7
|
1.0
|
C11
|
C:C2F302
|
2.5
|
53.8
|
1.0
|
N5
|
C:C2F302
|
2.6
|
53.9
|
1.0
|
O4
|
C:UFP301
|
2.6
|
44.9
|
1.0
|
O
|
C:HOH416
|
3.3
|
41.6
|
1.0
|
C6
|
C:C2F302
|
3.3
|
52.7
|
1.0
|
OH
|
C:TYR94
|
3.5
|
34.9
|
1.0
|
N3
|
C:UFP301
|
3.6
|
46.8
|
1.0
|
C4A
|
C:C2F302
|
3.7
|
54.6
|
1.0
|
N1
|
C:UFP301
|
3.7
|
54.4
|
1.0
|
O
|
C:HOH415
|
3.8
|
46.5
|
1.0
|
CB
|
C:CYS146
|
3.9
|
41.9
|
1.0
|
C7
|
C:C2F302
|
4.0
|
48.5
|
1.0
|
SG
|
C:CYS146
|
4.0
|
57.1
|
1.0
|
C2
|
C:UFP301
|
4.2
|
50.4
|
1.0
|
CZ2
|
C:TRP80
|
4.3
|
36.0
|
1.0
|
CD2
|
C:HIS147
|
4.3
|
37.7
|
1.0
|
CZ
|
C:TYR94
|
4.5
|
34.2
|
1.0
|
O4
|
C:C2F302
|
4.5
|
51.4
|
1.0
|
C4
|
C:C2F302
|
4.5
|
51.1
|
1.0
|
NE2
|
C:HIS147
|
4.5
|
35.4
|
1.0
|
C8A
|
C:C2F302
|
4.5
|
54.7
|
1.0
|
N8
|
C:C2F302
|
4.5
|
54.6
|
1.0
|
C9
|
C:C2F302
|
4.5
|
48.1
|
1.0
|
N10
|
C:C2F302
|
4.5
|
51.8
|
1.0
|
CH2
|
C:TRP80
|
4.6
|
35.2
|
1.0
|
O4'
|
C:UFP301
|
4.7
|
54.7
|
1.0
|
CE2
|
C:TYR94
|
4.7
|
30.9
|
1.0
|
C1'
|
C:UFP301
|
4.8
|
51.7
|
1.0
|
N
|
C:CYS146
|
5.0
|
35.8
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 4fog
Go back to
Fluorine Binding Sites List in 4fog
Fluorine binding site 4 out
of 4 in the Crystal Structure of Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid
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 Mtb Thya in Complex with 5-Fluoro-Dump and 5- Methyltetrahydrofolic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F301
b:46.0
occ:0.77
|
F5
|
D:UFP301
|
0.0
|
46.0
|
0.8
|
C5
|
D:UFP301
|
1.4
|
46.4
|
0.8
|
C4
|
D:UFP301
|
2.4
|
37.5
|
0.8
|
C6
|
D:UFP301
|
2.4
|
47.6
|
0.8
|
N5
|
D:C2F302
|
2.8
|
56.6
|
1.0
|
C11
|
D:C2F302
|
3.0
|
54.7
|
1.0
|
O4
|
D:UFP301
|
3.2
|
42.8
|
0.8
|
O
|
D:HOH419
|
3.2
|
37.5
|
1.0
|
C6
|
D:C2F302
|
3.2
|
52.1
|
1.0
|
OH
|
D:TYR94
|
3.5
|
37.1
|
1.0
|
N3
|
D:UFP301
|
3.6
|
38.9
|
0.8
|
C7
|
D:C2F302
|
3.6
|
48.9
|
1.0
|
N1
|
D:UFP301
|
3.7
|
47.0
|
0.8
|
C4A
|
D:C2F302
|
3.8
|
50.4
|
1.0
|
SG
|
D:CYS146
|
3.9
|
46.2
|
1.0
|
CZ2
|
D:TRP80
|
4.0
|
39.8
|
1.0
|
CH2
|
D:TRP80
|
4.0
|
39.6
|
1.0
|
C2
|
D:UFP301
|
4.2
|
37.7
|
0.8
|
CB
|
D:CYS146
|
4.3
|
34.2
|
1.0
|
CE2
|
D:TYR94
|
4.3
|
34.0
|
1.0
|
CZ
|
D:TYR94
|
4.3
|
35.2
|
1.0
|
N8
|
D:C2F302
|
4.3
|
53.9
|
1.0
|
C8A
|
D:C2F302
|
4.5
|
50.1
|
1.0
|
C9
|
D:C2F302
|
4.5
|
51.1
|
1.0
|
CD2
|
D:HIS147
|
4.6
|
33.4
|
1.0
|
O4'
|
D:UFP301
|
4.7
|
47.8
|
0.8
|
O
|
D:HOH484
|
4.7
|
45.9
|
1.0
|
C1'
|
D:UFP301
|
4.8
|
43.5
|
0.8
|
C4
|
D:C2F302
|
4.8
|
50.0
|
1.0
|
NE2
|
D:HIS147
|
4.8
|
32.5
|
1.0
|
N10
|
D:C2F302
|
4.8
|
45.3
|
1.0
|
O4
|
D:C2F302
|
4.9
|
48.5
|
1.0
|
CE2
|
D:TRP80
|
5.0
|
38.7
|
1.0
|
|
Reference:
M.C.M.Reddy,
J.B.Bruning,
J.C.Sacchettini.
Crystal Structure of Binary and Ternary Complexes of Thymidylate Synthase (Thya) From Mycobacterium Tuberculosis: Insights Into the Selectivity and Mode of Inhibition To Be Published.
Page generated: Thu Aug 1 01:38:27 2024
|