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Fluorine in PDB 5xii: Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6

Enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6

All present enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6, PDB code: 5xii was solved by V.Jain, Y.Manickam, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.29 / 2.17
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.600, 90.730, 92.996, 89.94, 99.37, 104.31
R / Rfree (%) 17.5 / 22.4

Other elements in 5xii:

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Chlorine (Cl) 15 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 (pdb code 5xii). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6, PDB code: 5xii:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5xii

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Fluorine binding site 1 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:24.9
occ:0.50
 F01 A:86X1004 0.0 24.9 0.5
F01 A:86X1004 0.2 20.1 0.5
C02 A:86X1004 1.4 25.1 0.5
C02 A:86X1004 1.4 21.3 0.5
C03 A:86X1004 2.3 22.3 0.5
C03 A:86X1004 2.4 26.4 0.5
C08 A:86X1004 2.4 23.5 0.5
C08 A:86X1004 2.5 20.3 0.5
CL4 A:86X1004 2.8 27.3 0.5
CL4 A:86X1004 3.0 33.0 0.5
O A:PHE415 3.3 28.8 1.0
CG2 A:VAL419 3.4 21.7 1.0
CB A:PRO438 3.5 17.5 1.0
C05 A:86X1004 3.6 21.1 0.5
C05 A:86X1004 3.6 24.6 0.5
C07 A:86X1004 3.7 23.6 0.5
CB A:PHE415 3.7 32.5 1.0
CB A:GLU418 3.7 24.1 1.0
C07 A:86X1004 3.7 20.7 0.5
CG A:PRO438 3.8 18.3 1.0
C A:PHE415 4.0 32.8 1.0
OE1 A:GLU418 4.1 27.0 1.0
N A:VAL419 4.1 21.9 1.0
C06 A:86X1004 4.1 23.2 0.5
C06 A:86X1004 4.2 20.6 0.5
C A:GLU418 4.2 21.8 1.0
CA A:PHE415 4.4 35.8 1.0
CA A:GLU418 4.5 22.6 1.0
CG A:PHE415 4.5 33.3 1.0
CA A:VAL419 4.5 20.3 1.0
CB A:VAL419 4.6 20.0 1.0
O A:GLU418 4.6 23.7 1.0
CD1 A:PHE415 4.8 33.8 1.0
N09 A:86X1004 4.8 23.1 0.5
CG A:GLU418 4.8 26.1 1.0
CD A:GLU418 4.9 28.8 1.0
N A:GLU418 4.9 23.1 1.0
N09 A:86X1004 4.9 20.7 0.5
CG A:ARG470 4.9 18.8 1.0
CA A:PRO438 4.9 17.6 1.0

Fluorine binding site 2 out of 8 in 5xii

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Fluorine binding site 2 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:20.1
occ:0.50
 F01 A:86X1004 0.0 20.1 0.5
F01 A:86X1004 0.2 24.9 0.5
C02 A:86X1004 1.3 25.1 0.5
C02 A:86X1004 1.4 21.3 0.5
C08 A:86X1004 2.3 23.5 0.5
C03 A:86X1004 2.4 22.3 0.5
C08 A:86X1004 2.4 20.3 0.5
C03 A:86X1004 2.4 26.4 0.5
CL4 A:86X1004 3.0 27.3 0.5
CL4 A:86X1004 3.1 33.0 0.5
CB A:PRO438 3.3 17.5 1.0
O A:PHE415 3.4 28.8 1.0
CG2 A:VAL419 3.5 21.7 1.0
C07 A:86X1004 3.6 23.6 0.5
C05 A:86X1004 3.6 21.1 0.5
C07 A:86X1004 3.7 20.7 0.5
CB A:GLU418 3.7 24.1 1.0
C05 A:86X1004 3.7 24.6 0.5
CG A:PRO438 3.7 18.3 1.0
CB A:PHE415 3.8 32.5 1.0
OE1 A:GLU418 4.0 27.0 1.0
C06 A:86X1004 4.1 23.2 0.5
C06 A:86X1004 4.1 20.6 0.5
N A:VAL419 4.2 21.9 1.0
C A:GLU418 4.2 21.8 1.0
C A:PHE415 4.2 32.8 1.0
CA A:GLU418 4.5 22.6 1.0
CA A:VAL419 4.5 20.3 1.0
O A:GLU418 4.6 23.7 1.0
CA A:PHE415 4.6 35.8 1.0
CG A:PHE415 4.6 33.3 1.0
CB A:VAL419 4.6 20.0 1.0
N09 A:86X1004 4.7 23.1 0.5
CG A:ARG470 4.7 18.8 1.0
CA A:PRO438 4.8 17.6 1.0
N09 A:86X1004 4.8 20.7 0.5
CG A:GLU418 4.8 26.1 1.0
CD A:GLU418 4.8 28.8 1.0
CD1 A:PHE415 4.8 33.8 1.0
N A:GLU418 4.9 23.1 1.0

Fluorine binding site 3 out of 8 in 5xii

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Fluorine binding site 3 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1004

b:23.7
occ:0.50
 F01 B:86X1004 0.0 23.7 0.5
F01 B:86X1004 0.5 30.0 0.5
C02 B:86X1004 1.4 22.9 0.5
C02 B:86X1004 1.6 29.6 0.5
C08 B:86X1004 2.4 28.1 0.5
C03 B:86X1004 2.4 22.7 0.5
C08 B:86X1004 2.4 21.6 0.5
C03 B:86X1004 2.7 30.5 0.5
CL4 B:86X1004 3.0 26.7 0.5
CL4 B:86X1004 3.4 39.4 0.5
O B:PHE415 3.4 37.8 1.0
CB B:PRO438 3.5 19.7 1.0
CG2 B:VAL419 3.6 21.4 1.0
CB B:GLU418 3.6 24.6 1.0
C05 B:86X1004 3.6 22.3 0.5
C07 B:86X1004 3.7 21.4 0.5
C07 B:86X1004 3.7 27.6 0.5
CB B:PHE415 3.8 41.9 1.0
CG B:PRO438 3.8 21.3 1.0
C05 B:86X1004 3.9 29.5 0.5
OE1 B:GLU418 4.0 28.7 1.0
C06 B:86X1004 4.1 21.5 0.5
C B:PHE415 4.2 39.6 1.0
C B:GLU418 4.2 23.2 1.0
N B:VAL419 4.3 21.6 1.0
C06 B:86X1004 4.3 27.8 0.5
CA B:PHE415 4.4 43.3 1.0
CA B:GLU418 4.4 24.8 1.0
CG B:PHE415 4.4 42.3 1.0
O B:GLU418 4.6 22.8 1.0
CD1 B:PHE415 4.6 39.7 1.0
CA B:VAL419 4.6 21.2 1.0
CG B:GLU418 4.7 25.5 1.0
CG B:ARG470 4.7 20.0 1.0
N09 B:86X1004 4.8 27.0 0.5
CB B:VAL419 4.8 21.3 1.0
CD B:GLU418 4.8 27.8 1.0
N09 B:86X1004 4.8 21.1 0.5
N B:GLU418 4.8 27.6 1.0
CA B:PRO438 5.0 20.6 1.0

Fluorine binding site 4 out of 8 in 5xii

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Fluorine binding site 4 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


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 Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1004

b:30.0
occ:0.50
 F01 B:86X1004 0.0 30.0 0.5
F01 B:86X1004 0.5 23.7 0.5
C02 B:86X1004 1.2 22.9 0.5
C02 B:86X1004 1.4 29.6 0.5
C03 B:86X1004 2.0 22.7 0.5
C03 B:86X1004 2.4 30.5 0.5
C08 B:86X1004 2.4 28.1 0.5
C08 B:86X1004 2.4 21.6 0.5
CL4 B:86X1004 2.5 26.7 0.5
CL4 B:86X1004 3.0 39.4 0.5
C05 B:86X1004 3.3 22.3 0.5
O B:PHE415 3.4 37.8 1.0
CB B:PHE415 3.5 41.9 1.0
CG2 B:VAL419 3.5 21.4 1.0
CB B:PRO438 3.6 19.7 1.0
C07 B:86X1004 3.6 21.4 0.5
C05 B:86X1004 3.6 29.5 0.5
C07 B:86X1004 3.7 27.6 0.5
CG B:PRO438 3.7 21.3 1.0
C06 B:86X1004 3.9 21.5 0.5
CB B:GLU418 4.0 24.6 1.0
C B:PHE415 4.0 39.6 1.0
C06 B:86X1004 4.1 27.8 0.5
CG B:PHE415 4.2 42.3 1.0
CA B:PHE415 4.2 43.3 1.0
OE1 B:GLU418 4.4 28.7 1.0
N B:VAL419 4.5 21.6 1.0
CD1 B:PHE415 4.5 39.7 1.0
C B:GLU418 4.5 23.2 1.0
CA B:GLU418 4.7 24.8 1.0
CB B:VAL419 4.8 21.3 1.0
CA B:VAL419 4.8 21.2 1.0
N09 B:86X1004 4.8 27.0 0.5
N09 B:86X1004 4.8 21.1 0.5
O B:GLU418 4.9 22.8 1.0

Fluorine binding site 5 out of 8 in 5xii

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Fluorine binding site 5 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1004

b:26.0
occ:0.50
 F01 C:86X1004 0.0 26.0 0.5
F01 C:86X1004 0.1 25.8 0.5
C02 C:86X1004 1.3 27.1 0.5
C02 C:86X1004 1.4 27.3 0.5
C03 C:86X1004 2.3 28.1 0.5
C08 C:86X1004 2.4 25.6 0.5
C03 C:86X1004 2.4 28.2 0.5
C08 C:86X1004 2.4 25.8 0.5
CL4 C:86X1004 2.9 37.6 0.5
CL4 C:86X1004 3.0 38.2 0.5
CB C:PRO438 3.3 21.4 1.0
O C:PHE415 3.4 34.5 1.0
CG2 C:VAL419 3.4 20.9 1.0
CG C:PRO438 3.5 21.2 1.0
C05 C:86X1004 3.6 26.5 0.5
C07 C:86X1004 3.6 25.7 0.5
C05 C:86X1004 3.6 27.3 0.5
C07 C:86X1004 3.7 26.7 0.5
CB C:GLU418 3.8 25.6 1.0
CB C:PHE415 3.9 41.0 1.0
C06 C:86X1004 4.1 25.9 0.5
C C:PHE415 4.1 42.0 1.0
C06 C:86X1004 4.1 26.5 0.5
OE1 C:GLU418 4.2 29.8 1.0
N C:VAL419 4.2 22.0 1.0
C C:GLU418 4.3 24.1 1.0
CA C:VAL419 4.5 21.5 1.0
CA C:PHE415 4.5 44.9 1.0
CA C:GLU418 4.5 25.2 1.0
CB C:VAL419 4.6 21.9 1.0
CG C:PHE415 4.6 41.2 1.0
O C:GLU418 4.7 24.6 1.0
N09 C:86X1004 4.8 26.4 0.5
N09 C:86X1004 4.8 27.3 0.5
CA C:PRO438 4.8 20.7 1.0
CG C:ARG470 4.8 21.5 1.0
CD C:PRO438 4.9 20.7 1.0
N C:GLU418 4.9 24.7 1.0
CG C:GLU418 4.9 29.3 1.0
CD1 C:PHE415 4.9 39.6 1.0
CD C:GLU418 5.0 32.1 1.0

Fluorine binding site 6 out of 8 in 5xii

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Fluorine binding site 6 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1004

b:25.8
occ:0.50
 F01 C:86X1004 0.0 25.8 0.5
F01 C:86X1004 0.1 26.0 0.5
C02 C:86X1004 1.4 27.1 0.5
C02 C:86X1004 1.4 27.3 0.5
C03 C:86X1004 2.4 28.1 0.5
C08 C:86X1004 2.4 25.6 0.5
C08 C:86X1004 2.4 25.8 0.5
C03 C:86X1004 2.5 28.2 0.5
CL4 C:86X1004 3.0 37.6 0.5
CL4 C:86X1004 3.0 38.2 0.5
O C:PHE415 3.3 34.5 1.0
CG2 C:VAL419 3.4 20.9 1.0
CB C:PRO438 3.4 21.4 1.0
CG C:PRO438 3.6 21.2 1.0
C05 C:86X1004 3.7 26.5 0.5
C07 C:86X1004 3.7 25.7 0.5
CB C:GLU418 3.7 25.6 1.0
C07 C:86X1004 3.7 26.7 0.5
C05 C:86X1004 3.7 27.3 0.5
CB C:PHE415 3.8 41.0 1.0
C C:PHE415 4.0 42.0 1.0
OE1 C:GLU418 4.1 29.8 1.0
N C:VAL419 4.1 22.0 1.0
C06 C:86X1004 4.1 25.9 0.5
C C:GLU418 4.2 24.1 1.0
C06 C:86X1004 4.2 26.5 0.5
CA C:PHE415 4.4 44.9 1.0
CA C:GLU418 4.4 25.2 1.0
CA C:VAL419 4.4 21.5 1.0
CB C:VAL419 4.5 21.9 1.0
CG C:PHE415 4.6 41.2 1.0
O C:GLU418 4.6 24.6 1.0
N C:GLU418 4.8 24.7 1.0
CG C:GLU418 4.8 29.3 1.0
N09 C:86X1004 4.8 26.4 0.5
CG C:ARG470 4.8 21.5 1.0
N09 C:86X1004 4.8 27.3 0.5
CD C:GLU418 4.9 32.1 1.0
CD1 C:PHE415 4.9 39.6 1.0
CA C:PRO438 4.9 20.7 1.0

Fluorine binding site 7 out of 8 in 5xii

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Fluorine binding site 7 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1004

b:24.3
occ:0.50
 F01 D:86X1004 0.0 24.3 0.5
F01 D:86X1004 0.4 25.1 0.5
C02 D:86X1004 1.4 26.2 0.5
C02 D:86X1004 1.4 27.9 0.5
C08 D:86X1004 2.2 27.0 0.5
C03 D:86X1004 2.4 27.1 0.5
C08 D:86X1004 2.4 25.2 0.5
C03 D:86X1004 2.6 29.1 0.5
CL4 D:86X1004 3.0 31.6 0.5
CL4 D:86X1004 3.3 32.8 0.5
O D:PHE415 3.4 36.5 1.0
C07 D:86X1004 3.5 27.6 0.5
CB D:PRO438 3.5 19.3 1.0
CG2 D:VAL419 3.6 20.5 1.0
C05 D:86X1004 3.6 25.8 0.5
C07 D:86X1004 3.7 25.3 0.5
CB D:GLU418 3.7 25.0 1.0
CG D:PRO438 3.7 20.1 1.0
OE1 D:GLU418 3.8 26.8 1.0
C05 D:86X1004 3.8 28.0 0.5
CB D:PHE415 3.8 40.2 1.0
C06 D:86X1004 4.1 27.6 0.5
C D:PHE415 4.1 39.8 1.0
C06 D:86X1004 4.1 25.3 0.5
N D:VAL419 4.1 20.9 1.0
C D:GLU418 4.2 20.8 1.0
CA D:GLU418 4.4 23.6 1.0
CA D:PHE415 4.4 41.8 1.0
CG D:PHE415 4.5 37.5 1.0
O D:GLU418 4.5 18.6 1.0
CA D:VAL419 4.6 20.4 1.0
CD D:GLU418 4.6 28.3 1.0
CG D:GLU418 4.6 25.8 1.0
N09 D:86X1004 4.6 27.7 0.5
CD1 D:PHE415 4.6 35.8 1.0
CG D:ARG470 4.7 18.2 1.0
CB D:VAL419 4.7 19.9 1.0
N D:GLU418 4.8 24.0 1.0
N09 D:86X1004 4.8 24.8 0.5

Fluorine binding site 8 out of 8 in 5xii

Go back to Fluorine Binding Sites List in 5xii
Fluorine binding site 8 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1004

b:25.1
occ:0.50
 F01 D:86X1004 0.0 25.1 0.5
F01 D:86X1004 0.4 24.3 0.5
C02 D:86X1004 1.4 27.9 0.5
C02 D:86X1004 1.4 26.2 0.5
C03 D:86X1004 2.2 27.1 0.5
C03 D:86X1004 2.4 29.1 0.5
C08 D:86X1004 2.4 27.0 0.5
CL4 D:86X1004 2.6 31.6 0.5
C08 D:86X1004 2.6 25.2 0.5
CL4 D:86X1004 3.0 32.8 0.5
CG2 D:VAL419 3.3 20.5 1.0
O D:PHE415 3.4 36.5 1.0
CG D:PRO438 3.5 20.1 1.0
CB D:PRO438 3.5 19.3 1.0
C05 D:86X1004 3.6 25.8 0.5
C05 D:86X1004 3.6 28.0 0.5
C07 D:86X1004 3.7 27.6 0.5
CB D:PHE415 3.8 40.2 1.0
C07 D:86X1004 3.8 25.3 0.5
CB D:GLU418 3.9 25.0 1.0
C D:PHE415 4.1 39.8 1.0
N D:VAL419 4.1 20.9 1.0
OE1 D:GLU418 4.1 26.8 1.0
C06 D:86X1004 4.1 27.6 0.5
C06 D:86X1004 4.2 25.3 0.5
C D:GLU418 4.3 20.8 1.0
CA D:PHE415 4.5 41.8 1.0
CA D:VAL419 4.5 20.4 1.0
CG D:PHE415 4.5 37.5 1.0
CB D:VAL419 4.5 19.9 1.0
CA D:GLU418 4.6 23.6 1.0
O D:GLU418 4.6 18.6 1.0
CD1 D:PHE415 4.8 35.8 1.0
N09 D:86X1004 4.8 27.7 0.5
CD D:PRO438 4.9 19.3 1.0
CG D:GLU418 4.9 25.8 1.0
N D:GLU418 4.9 24.0 1.0
CD D:GLU418 4.9 28.3 1.0
CG D:ARG470 5.0 18.2 1.0

Reference:

V.Jain, M.Yogavel, H.Kikuchi, Y.Oshima, N.Hariguchi, M.Matsumoto, P.Goel, B.Touquet, R.S.Jumani, F.Tacchini-Cottier, K.Harlos, C.D.Huston, M.A.Hakimi, A.Sharma. Targeting Prolyl-Trna Synthetase to Accelerate Drug Discovery Against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis Structure V. 25 1495 2017.
ISSN: ISSN 1878-4186
PubMed: 28867614
DOI: 10.1016/J.STR.2017.07.015
Page generated: Thu Aug 1 16:53:26 2024

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