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Fluorine in PDB 7f9u: Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone

Protein crystallography data

The structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone, PDB code: 7f9u was solved by Y.Manickam, N.Malhotra, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.57 / 2.80
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 76.573, 76.573, 403.841, 90, 90, 90
R / Rfree (%) 16.4 / 22.4

Other elements in 7f9u:

The structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone also contains other interesting chemical elements:

Bromine (Br) 7 atoms
Calcium (Ca) 3 atoms
Chlorine (Cl) 12 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone (pdb code 7f9u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone, PDB code: 7f9u:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7f9u

Go back to Fluorine Binding Sites List in 7f9u
Fluorine binding site 1 out of 4 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:40.4
occ:0.94
 F A:1TI902 0.0 40.4 0.9
C10 A:1TI902 1.3 19.8 0.9
C9 A:1TI902 2.3 19.8 0.9
C11 A:1TI902 2.3 19.7 0.9
CB A:PRO476 3.3 29.3 1.0
CA A:PRO476 3.5 30.3 1.0
C12 A:1TI902 3.6 19.7 0.9
C8 A:1TI902 3.6 27.1 0.9
N A:PRO476 3.7 33.5 1.0
O A:LYS474 3.7 32.3 1.0
CG A:PRO476 3.8 29.3 1.0
CD A:PRO476 3.8 31.9 1.0
CG A:ARG483 4.0 31.4 1.0
C13 A:1TI902 4.1 19.7 0.9
O A:GLU472 4.1 43.5 1.0
O A:ARG481 4.1 26.8 1.0
C A:GLN475 4.1 38.2 1.0
NE A:ARG483 4.2 45.6 1.0
N A:ARG483 4.3 19.3 1.0
C A:LYS474 4.3 36.6 1.0
O A:GLN475 4.4 40.8 1.0
CA A:THR482 4.4 20.4 1.0
C A:THR482 4.5 22.1 1.0
C A:ARG481 4.6 28.4 1.0
CA A:GLY363 4.6 35.0 1.0
CD A:ARG483 4.7 39.3 1.0
N A:THR482 4.7 18.2 1.0
C14 A:1TI902 4.8 28.3 0.9
CZ A:ARG483 4.8 48.9 1.0
C7 A:1TI902 4.8 19.7 0.9
N A:GLN475 4.8 40.3 1.0
CB A:ARG483 4.8 20.4 1.0
CA A:ARG483 4.8 19.9 1.0
N A:LYS474 4.9 47.3 1.0
NH2 A:ARG483 4.9 52.0 1.0
CA A:GLN475 4.9 41.4 1.0
C A:PRO476 5.0 25.2 1.0

Fluorine binding site 2 out of 4 in 7f9u

Go back to Fluorine Binding Sites List in 7f9u
Fluorine binding site 2 out of 4 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F902

b:35.6
occ:1.00
 F B:1TI902 0.0 35.6 1.0
C10 B:1TI902 1.4 32.7 1.0
C11 B:1TI902 2.3 19.9 1.0
C9 B:1TI902 2.3 29.8 1.0
CB B:PRO476 3.1 30.4 1.0
CA B:PRO476 3.4 19.1 1.0
CD B:PRO476 3.5 32.1 1.0
N B:PRO476 3.5 35.4 1.0
C12 B:1TI902 3.6 26.9 1.0
C8 B:1TI902 3.6 25.2 1.0
NE B:ARG483 3.6 39.5 1.0
O B:LYS474 3.7 33.4 1.0
CG B:PRO476 3.7 19.7 1.0
CG B:ARG483 3.7 25.6 1.0
O B:GLU472 4.0 48.8 1.0
C13 B:1TI902 4.1 23.8 1.0
C B:GLN475 4.2 35.6 1.0
O B:ARG481 4.2 22.2 1.0
N B:ARG483 4.2 19.3 1.0
CD B:ARG483 4.3 30.9 1.0
CA B:GLY363 4.4 37.2 1.0
CA B:THR482 4.4 18.5 1.0
C B:THR482 4.4 27.8 1.0
C B:LYS474 4.5 39.3 1.0
NH2 B:ARG483 4.5 48.7 1.0
CZ B:ARG483 4.5 46.3 1.0
O B:GLN475 4.6 35.5 1.0
CB B:ARG483 4.7 22.9 1.0
C B:ARG481 4.7 21.4 1.0
CA B:ARG483 4.8 22.3 1.0
C14 B:1TI902 4.8 32.6 1.0
C7 B:1TI902 4.9 23.8 1.0
N B:LYS474 4.9 69.2 1.0
N B:THR482 4.9 18.2 1.0
C B:PRO476 4.9 24.4 1.0
C B:GLU472 4.9 56.9 1.0
CB B:GLU472 5.0 48.0 1.0
O B:GLY363 5.0 26.8 1.0

Fluorine binding site 3 out of 4 in 7f9u

Go back to Fluorine Binding Sites List in 7f9u
Fluorine binding site 3 out of 4 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F902

b:31.0
occ:0.82
 F C:1TI902 0.0 31.0 0.8
C10 C:1TI902 1.4 25.1 0.8
C9 C:1TI902 2.3 24.7 0.8
C11 C:1TI902 2.3 25.4 0.8
CA C:PRO476 3.3 33.6 1.0
N C:PRO476 3.4 35.9 1.0
CB C:PRO476 3.4 29.7 1.0
O C:LYS474 3.6 38.9 1.0
CD C:PRO476 3.6 38.6 1.0
C12 C:1TI902 3.6 25.4 0.8
C8 C:1TI902 3.6 25.8 0.8
NE C:ARG483 3.7 50.5 1.0
O C:GLU472 3.8 52.1 1.0
C C:GLN475 4.0 37.4 1.0
O C:ARG481 4.0 31.4 1.0
CG C:PRO476 4.0 25.2 1.0
C13 C:1TI902 4.1 25.0 0.8
NH2 C:ARG483 4.1 63.4 1.0
C C:LYS474 4.2 38.8 1.0
CG C:ARG483 4.3 40.0 1.0
O C:GLN475 4.4 35.7 1.0
CZ C:ARG483 4.4 58.5 1.0
CD C:ARG483 4.6 47.4 1.0
C C:GLU472 4.6 41.6 1.0
N C:LYS474 4.7 34.5 1.0
CA C:THR482 4.7 30.2 1.0
C C:THR482 4.7 29.4 1.0
N C:ARG483 4.7 28.8 1.0
C C:ARG481 4.8 29.0 1.0
N C:GLN475 4.8 43.9 1.0
CA C:GLN475 4.8 43.8 1.0
CA C:GLY363 4.8 41.6 1.0
CB C:GLU472 4.8 39.2 1.0
C14 C:1TI902 4.8 25.8 0.8
C C:PRO476 4.8 24.6 1.0
C7 C:1TI902 4.9 24.2 0.8

Fluorine binding site 4 out of 4 in 7f9u

Go back to Fluorine Binding Sites List in 7f9u
Fluorine binding site 4 out of 4 in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F902

b:36.2
occ:1.00
 F D:1TI902 0.0 36.2 1.0
C10 D:1TI902 1.4 36.3 1.0
C9 D:1TI902 2.3 37.6 1.0
C11 D:1TI902 2.3 37.5 1.0
CB D:PRO476 3.1 34.3 1.0
O D:LYS474 3.1 45.7 1.0
CA D:PRO476 3.3 25.7 1.0
N D:PRO476 3.4 59.6 1.0
CD D:PRO476 3.4 26.6 1.0
CG D:PRO476 3.6 25.9 1.0
C12 D:1TI902 3.6 41.2 1.0
C8 D:1TI902 3.6 35.3 1.0
NE D:ARG483 3.8 38.1 1.0
O D:GLU472 3.9 43.0 1.0
C D:LYS474 4.1 43.0 1.0
C13 D:1TI902 4.1 38.8 1.0
C D:GLN475 4.1 50.3 1.0
CG D:ARG483 4.3 33.8 1.0
NH2 D:ARG483 4.4 53.9 1.0
O D:ARG481 4.5 34.7 1.0
CZ D:ARG483 4.5 47.2 1.0
N D:ARG483 4.5 29.4 1.0
CA D:THR482 4.6 23.7 1.0
O D:GLN475 4.6 51.0 1.0
C D:THR482 4.6 33.6 1.0
CA D:GLY363 4.6 25.0 1.0
CD D:ARG483 4.6 35.0 1.0
N D:LYS474 4.7 36.3 1.0
C D:PRO476 4.8 25.5 1.0
C14 D:1TI902 4.8 46.5 1.0
C D:GLU472 4.8 40.6 1.0
C7 D:1TI902 4.9 29.8 1.0
N D:GLN475 4.9 45.0 1.0
CA D:LYS474 4.9 40.2 1.0
CA D:GLN475 4.9 49.1 1.0
C D:ARG481 4.9 38.7 1.0
CB D:GLU472 4.9 35.3 1.0
CB D:ARG483 5.0 29.5 1.0

Reference:

N.Malhotra, Y.Manickam, A.Sharma. Tgprs with Double Inhibitors To Be Published.
Page generated: Tue Jul 15 19:25:51 2025

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