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Fluorine in PDB 7f9v: 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: 7f9v 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) 75.07 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.067, 82.981, 105.521, 90, 103.08, 90
R / Rfree (%) 17.2 / 19.7

Other elements in 7f9v:

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

Bromine (Br) 8 atoms
Chlorine (Cl) 2 atoms
Iodine (I) 10 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 7f9v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor T35 and Halofuginone, PDB code: 7f9v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 7f9v

Go back to Fluorine Binding Sites List in 7f9v
Fluorine binding site 1 out of 5 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:F901

b:44.0
occ:1.00
 F A:1TI901 0.0 44.0 1.0
C10 A:1TI901 1.4 44.0 1.0
C11 A:1TI901 2.3 38.7 1.0
C9 A:1TI901 2.4 34.1 1.0
CB A:PRO476 3.1 42.4 1.0
O A:LYS474 3.2 51.0 1.0
CA A:PRO476 3.3 39.7 1.0
N A:PRO476 3.5 41.5 1.0
C12 A:1TI901 3.6 42.2 1.0
C8 A:1TI901 3.6 33.8 1.0
CD A:PRO476 3.7 43.6 1.0
CG A:PRO476 3.8 43.4 1.0
CG A:ARG483 3.9 47.5 1.0
O A:ARG481 4.0 32.8 1.0
C A:GLN475 4.0 37.5 1.0
C13 A:1TI901 4.1 34.1 1.0
O A:GLU472 4.2 54.9 1.0
C A:LYS474 4.2 48.8 1.0
CA A:GLY363 4.3 45.8 1.0
N A:ARG483 4.3 32.8 1.0
O A:GLN475 4.4 40.8 1.0
CA A:THR482 4.4 35.3 1.0
C A:THR482 4.5 32.5 1.0
C A:ARG481 4.6 32.2 1.0
NE A:ARG483 4.7 57.9 1.0
N A:THR482 4.8 32.3 1.0
C A:PRO476 4.8 40.8 1.0
C14 A:1TI901 4.8 44.1 1.0
CD A:ARG483 4.9 48.5 1.0
C7 A:1TI901 4.9 36.5 1.0
CA A:GLN475 4.9 48.2 1.0
CA A:ARG483 4.9 33.1 1.0
CB A:ARG483 5.0 34.0 1.0
N A:GLN475 5.0 47.9 1.0

Fluorine binding site 2 out of 5 in 7f9v

Go back to Fluorine Binding Sites List in 7f9v
Fluorine binding site 2 out of 5 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
A:F912

b:41.6
occ:1.00
 N A:ILE655 3.0 33.6 1.0
O A:HOH1235 3.1 61.5 1.0
NZ A:LYS643 3.2 59.3 1.0
CE A:LYS643 3.5 53.8 1.0
CA A:ARG654 3.7 33.4 1.0
O A:ILE655 3.8 36.4 1.0
C A:ARG654 3.8 33.5 1.0
CA A:ILE655 3.9 33.8 1.0
CB A:ILE655 3.9 36.2 1.0
CD A:LYS643 3.9 42.0 1.0
CD A:ARG654 3.9 47.7 1.0
CG1 A:ILE655 4.2 39.5 1.0
C A:ILE655 4.3 35.8 1.0
O A:VAL653 4.4 32.7 1.0
CB A:ARG654 4.5 34.0 1.0
CG A:ARG654 4.5 38.0 1.0
NE A:ARG654 4.6 54.4 1.0
CD1 A:ILE655 4.8 37.8 1.0
N A:ARG654 4.8 35.9 1.0

Fluorine binding site 3 out of 5 in 7f9v

Go back to Fluorine Binding Sites List in 7f9v
Fluorine binding site 3 out of 5 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
A:F913

b:50.9
occ:1.00
 O A:HOH1271 2.8 56.4 1.0
O A:HOH1291 3.1 43.5 1.0
NZ A:LYS377 3.2 38.4 1.0
CD A:LYS377 3.8 35.1 1.0
O A:GLU376 3.9 27.5 1.0
CA A:LYS377 4.0 26.2 1.0
CE A:LYS377 4.0 42.2 1.0
CB A:ARG380 4.1 25.9 1.0
C A:GLU376 4.2 29.6 1.0
N A:LYS377 4.2 27.6 1.0
CG A:LYS377 4.2 33.4 1.0
O A:HOH1053 4.4 42.6 1.0
O A:HOH1247 4.4 47.5 1.0
CG A:ARG380 4.5 29.1 1.0
O A:HOH1083 4.5 32.7 1.0
CB A:LYS377 4.7 29.3 1.0
O A:HOH1264 4.8 60.1 1.0
CB A:GLU376 4.8 29.8 1.0
CZ A:ARG380 4.8 40.8 1.0
NH2 A:ARG380 5.0 42.0 1.0
NE A:ARG380 5.0 39.6 1.0
O A:LYS377 5.0 28.2 1.0
C A:LYS377 5.0 26.5 1.0

Fluorine binding site 4 out of 5 in 7f9v

Go back to Fluorine Binding Sites List in 7f9v
Fluorine binding site 4 out of 5 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
B:F902

b:43.4
occ:1.00
 F B:1TI902 0.0 43.4 1.0
C10 B:1TI902 1.4 40.0 1.0
C9 B:1TI902 2.3 35.9 1.0
C11 B:1TI902 2.3 37.0 1.0
O B:LYS474 3.2 62.4 1.0
CB B:PRO476 3.3 42.3 1.0
CA B:PRO476 3.4 43.0 1.0
N B:PRO476 3.6 42.9 1.0
C8 B:1TI902 3.6 41.4 1.0
C12 B:1TI902 3.6 42.5 1.0
CZ B:ARG483 3.7 69.0 1.0
CG B:ARG483 3.7 43.7 1.0
CD B:PRO476 3.9 48.5 1.0
NH1 B:ARG483 3.9 73.8 1.0
NH2 B:ARG483 3.9 69.1 1.0
NE B:ARG483 3.9 57.5 1.0
CG B:PRO476 4.0 48.0 1.0
C B:GLN475 4.0 47.1 1.0
O B:GLU472 4.1 51.6 1.0
C13 B:1TI902 4.1 36.3 1.0
O B:ARG481 4.1 36.5 1.0
C B:LYS474 4.3 62.2 1.0
O B:GLN475 4.3 43.1 1.0
N B:ARG483 4.4 34.0 1.0
CD B:ARG483 4.4 47.9 1.0
C B:THR482 4.6 35.3 1.0
CA B:THR482 4.6 33.4 1.0
C B:ARG481 4.7 40.6 1.0
CA B:GLY363 4.7 43.8 1.0
C14 B:1TI902 4.8 46.8 1.0
CA B:GLN475 4.9 53.9 1.0
C7 B:1TI902 4.9 35.2 1.0
CB B:ARG483 4.9 37.6 1.0
C B:PRO476 4.9 47.1 1.0
C B:GLU472 4.9 53.6 1.0
N B:THR482 4.9 38.2 1.0
CA B:ARG483 4.9 34.3 1.0
N B:GLN475 5.0 58.5 1.0

Fluorine binding site 5 out of 5 in 7f9v

Go back to Fluorine Binding Sites List in 7f9v
Fluorine binding site 5 out of 5 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 5 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:F910

b:58.0
occ:0.91
 N B:LEU583 3.2 46.3 1.0
CA B:ARG582 3.8 50.6 1.0
O B:HOH1175 3.8 49.7 1.0
C B:ARG582 4.0 46.9 1.0
CB B:ARG582 4.1 49.6 1.0
CD B:ARG582 4.1 59.0 1.0
CB B:LEU583 4.1 48.1 1.0
CG B:LEU583 4.2 51.4 1.0
CA B:LEU583 4.2 46.2 1.0
CD1 B:LEU583 4.4 52.4 1.0
O B:LEU583 4.5 44.7 1.0
CG B:ARG582 4.7 53.4 1.0
O B:LYS581 4.9 47.8 1.0
O B:HOH1092 4.9 55.9 1.0
C B:LEU583 4.9 40.9 1.0

Reference:

N.Malhotra, Y.Manickam, A.Sharma. Tgprs with Double Inhibitors To Be Published.
Page generated: Fri Aug 2 06:52:48 2024

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