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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

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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: Mon Jul 14 21:41:16 2025

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