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

Go back to Fluorine Binding Sites List in 5xii
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

Go back to Fluorine Binding Sites List in 5xii
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

Go back to Fluorine Binding Sites List in 5xii
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

Go back to Fluorine Binding Sites List in 5xii
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

Go back to Fluorine Binding Sites List in 5xii
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

Go back to Fluorine Binding Sites List in 5xii
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

Go back to Fluorine Binding Sites List in 5xii
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: Sun Dec 13 12:42:43 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy