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Chlorine 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:

Fluorine (F) 8 atoms
Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 15 binding sites of Chlorine where determined in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 6, PDB code: 5xii:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 15 in 5xii

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Chlorine binding site 1 out of 15 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 Chlorine with other atoms in the Cl 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:Cl1004

b:33.0
occ:0.50
 CL4 A:86X1004 0.0 33.0 0.5
CL4 A:86X1004 0.3 27.3 0.5
C03 A:86X1004 1.7 26.4 0.5
C03 A:86X1004 1.8 22.3 0.5
C05 A:86X1004 2.7 24.6 0.5
C02 A:86X1004 2.7 25.1 0.5
C05 A:86X1004 2.7 21.1 0.5
C02 A:86X1004 2.8 21.3 0.5
F01 A:86X1004 3.0 24.9 0.5
F01 A:86X1004 3.1 20.1 0.5
O A:HOH1351 3.2 39.9 1.0
O A:HOH1321 3.5 36.9 1.0
CG A:PRO438 3.8 18.3 1.0
CB A:PHE415 3.8 32.5 1.0
CG2 A:VAL419 3.8 21.7 1.0
C06 A:86X1004 4.0 23.2 0.5
C08 A:86X1004 4.0 23.5 0.5
C06 A:86X1004 4.0 20.6 0.5
O A:HOH1355 4.1 28.0 1.0
C08 A:86X1004 4.1 20.3 0.5
CD1 A:LEU405 4.1 24.3 1.0
CB A:PRO438 4.4 17.5 1.0
C07 A:86X1004 4.5 23.6 0.5
CG A:PHE415 4.6 33.3 1.0
C07 A:86X1004 4.6 20.7 0.5
O A:PHE415 4.7 28.8 1.0
CG A:LEU405 4.8 25.9 1.0
CD2 A:LEU405 4.8 23.3 1.0
C A:PHE415 4.8 32.8 1.0
CD2 A:PHE415 4.8 33.0 1.0
CA A:PHE415 4.9 35.8 1.0

Chlorine binding site 2 out of 15 in 5xii

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Chlorine binding site 2 out of 15 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 Chlorine with other atoms in the Cl 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:Cl1004

b:27.3
occ:0.50
 CL4 A:86X1004 0.0 27.3 0.5
CL4 A:86X1004 0.3 33.0 0.5
C03 A:86X1004 1.7 26.4 0.5
C03 A:86X1004 1.7 22.3 0.5
C02 A:86X1004 2.6 25.1 0.5
C05 A:86X1004 2.7 24.6 0.5
C05 A:86X1004 2.7 21.1 0.5
C02 A:86X1004 2.7 21.3 0.5
F01 A:86X1004 2.8 24.9 0.5
F01 A:86X1004 3.0 20.1 0.5
CG A:PRO438 3.4 18.3 1.0
O A:HOH1351 3.5 39.9 1.0
O A:HOH1321 3.6 36.9 1.0
CG2 A:VAL419 3.7 21.7 1.0
C08 A:86X1004 3.9 23.5 0.5
C06 A:86X1004 4.0 23.2 0.5
CB A:PHE415 4.0 32.5 1.0
C06 A:86X1004 4.0 20.6 0.5
C08 A:86X1004 4.0 20.3 0.5
O A:HOH1355 4.0 28.0 1.0
CD1 A:LEU405 4.0 24.3 1.0
CB A:PRO438 4.1 17.5 1.0
C07 A:86X1004 4.4 23.6 0.5
C07 A:86X1004 4.5 20.7 0.5
CD A:PRO438 4.7 17.4 1.0
CD2 A:LEU405 4.7 23.3 1.0
CG A:LEU405 4.7 25.9 1.0
CG A:PHE415 4.8 33.3 1.0
O A:PHE415 4.8 28.8 1.0
C A:PHE415 5.0 32.8 1.0

Chlorine binding site 3 out of 15 in 5xii

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Chlorine binding site 3 out of 15 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 Chlorine with other atoms in the Cl 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:Cl1004

b:26.7
occ:0.50
 CL4 B:86X1004 0.0 26.7 0.5
CL4 B:86X1004 0.6 39.4 0.5
C03 B:86X1004 1.7 22.7 0.5
C03 B:86X1004 1.8 30.5 0.5
C02 B:86X1004 2.5 29.6 0.5
F01 B:86X1004 2.5 30.0 0.5
C05 B:86X1004 2.7 22.3 0.5
C02 B:86X1004 2.7 22.9 0.5
F01 B:86X1004 3.0 23.7 0.5
C05 B:86X1004 3.0 29.5 0.5
CG B:PRO438 3.6 21.3 1.0
CB B:PHE415 3.7 41.9 1.0
CG2 B:VAL419 3.8 21.4 1.0
C08 B:86X1004 3.8 28.1 0.5
O B:HOH1243 3.9 48.7 1.0
C06 B:86X1004 4.0 21.5 0.5
C08 B:86X1004 4.0 21.6 0.5
CD1 B:LEU405 4.1 31.3 1.0
C06 B:86X1004 4.2 27.8 0.5
O B:HOH1244 4.2 32.0 1.0
CG B:PHE415 4.4 42.3 1.0
CB B:PRO438 4.4 19.7 1.0
C07 B:86X1004 4.5 27.6 0.5
C07 B:86X1004 4.5 21.4 0.5
CD2 B:PHE415 4.7 40.6 1.0
CG B:LEU405 4.7 31.4 1.0
O B:PHE415 4.7 37.8 1.0
C B:PHE415 4.8 39.6 1.0
CD2 B:LEU405 4.8 33.5 1.0
CA B:PHE415 4.9 43.3 1.0
CD B:PRO438 4.9 21.5 1.0

Chlorine binding site 4 out of 15 in 5xii

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Chlorine binding site 4 out of 15 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 Chlorine with other atoms in the Cl 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:Cl1004

b:39.4
occ:0.50
 CL4 B:86X1004 0.0 39.4 0.5
CL4 B:86X1004 0.6 26.7 0.5
C03 B:86X1004 1.7 30.5 0.5
C03 B:86X1004 1.8 22.7 0.5
C05 B:86X1004 2.5 22.3 0.5
C05 B:86X1004 2.7 29.5 0.5
C02 B:86X1004 2.7 29.6 0.5
F01 B:86X1004 3.0 30.0 0.5
C02 B:86X1004 3.0 22.9 0.5
F01 B:86X1004 3.4 23.7 0.5
CG B:PRO438 3.5 21.3 1.0
O B:HOH1244 3.6 32.0 1.0
CD1 B:LEU405 3.8 31.3 1.0
C06 B:86X1004 3.9 21.5 0.5
C06 B:86X1004 4.0 27.8 0.5
C08 B:86X1004 4.0 28.1 0.5
O B:HOH1243 4.0 48.7 1.0
CB B:PHE415 4.1 41.9 1.0
C08 B:86X1004 4.2 21.6 0.5
CG2 B:VAL419 4.3 21.4 1.0
CB B:PRO438 4.4 19.7 1.0
C07 B:86X1004 4.5 27.6 0.5
C07 B:86X1004 4.5 21.4 0.5
CG B:LEU405 4.6 31.4 1.0
CG B:PHE415 4.6 42.3 1.0
CD2 B:PHE415 4.7 40.6 1.0
CD B:PRO438 4.8 21.5 1.0
CD2 B:LEU405 4.8 33.5 1.0
C22 B:86X1004 4.9 21.2 0.5
O23 B:86X1004 4.9 19.9 0.5

Chlorine binding site 5 out of 15 in 5xii

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Chlorine binding site 5 out of 15 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 Chlorine with other atoms in the Cl 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
B:Cl1008

b:71.0
occ:1.00
 CG2 B:ILE524 4.4 30.2 1.0
CD1 B:ILE524 4.5 33.9 1.0
O B:ASP803 4.6 53.2 1.0
CB B:PRO801 4.7 32.7 1.0
CG B:PRO801 4.8 31.9 1.0
CG1 B:ILE524 4.9 31.0 1.0
O B:HOH1184 5.0 34.3 1.0

Chlorine binding site 6 out of 15 in 5xii

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Chlorine binding site 6 out of 15 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 Chlorine with other atoms in the Cl 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
B:Cl1009

b:71.8
occ:1.00
 CG B:PHE473 3.7 27.2 1.0
CD2 B:PHE473 3.8 28.2 1.0
CD1 B:PHE473 4.0 28.5 1.0
CB B:PHE473 4.1 26.6 1.0
O A:HOH1287 4.1 40.4 1.0
CE2 B:PHE473 4.2 30.6 1.0
CE1 B:PHE473 4.4 30.0 1.0
CB B:PRO417 4.5 29.0 1.0
CZ B:PHE473 4.5 29.7 1.0
CG B:PRO417 4.5 30.0 1.0
O A:HOH1105 4.5 39.2 1.0
O A:LYS821 4.8 49.3 1.0
O A:HOH1237 4.9 17.8 1.0

Chlorine binding site 7 out of 15 in 5xii

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Chlorine binding site 7 out of 15 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 Chlorine with other atoms in the Cl 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
C:Cl1004

b:38.2
occ:0.50
 CL4 C:86X1004 0.0 38.2 0.5
CL4 C:86X1004 0.2 37.6 0.5
C03 C:86X1004 1.7 28.1 0.5
C03 C:86X1004 1.7 28.2 0.5
C05 C:86X1004 2.6 26.5 0.5
C02 C:86X1004 2.7 27.3 0.5
C05 C:86X1004 2.7 27.3 0.5
C02 C:86X1004 2.7 27.1 0.5
F01 C:86X1004 3.0 26.0 0.5
F01 C:86X1004 3.0 25.8 0.5
CG C:PRO438 3.5 21.2 1.0
O C:HOH1240 3.8 39.7 1.0
CG2 C:VAL419 3.8 20.9 1.0
C06 C:86X1004 3.9 25.9 0.5
CD1 C:LEU405 3.9 32.0 1.0
CB C:PHE415 4.0 41.0 1.0
C08 C:86X1004 4.0 25.6 0.5
C06 C:86X1004 4.0 26.5 0.5
C08 C:86X1004 4.0 25.8 0.5
O C:HOH1243 4.0 36.0 1.0
CB C:PRO438 4.4 21.4 1.0
C07 C:86X1004 4.4 25.7 0.5
C07 C:86X1004 4.5 26.7 0.5
CD C:PRO438 4.7 20.7 1.0
CG C:PHE415 4.7 41.2 1.0
CG C:LEU405 4.7 36.0 1.0
O C:PHE415 4.8 34.5 1.0
CD2 C:LEU405 4.8 37.0 1.0
C C:PHE415 4.9 42.0 1.0
CD2 C:PHE415 4.9 39.1 1.0
C22 C:86X1004 5.0 24.8 0.5

Chlorine binding site 8 out of 15 in 5xii

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Chlorine binding site 8 out of 15 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 Chlorine with other atoms in the Cl 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
C:Cl1004

b:37.6
occ:0.50
 CL4 C:86X1004 0.0 37.6 0.5
CL4 C:86X1004 0.2 38.2 0.5
C03 C:86X1004 1.7 28.1 0.5
C03 C:86X1004 1.8 28.2 0.5
C02 C:86X1004 2.7 27.3 0.5
C05 C:86X1004 2.7 26.5 0.5
C02 C:86X1004 2.7 27.1 0.5
C05 C:86X1004 2.8 27.3 0.5
F01 C:86X1004 2.9 26.0 0.5
F01 C:86X1004 3.0 25.8 0.5
CG C:PRO438 3.5 21.2 1.0
CG2 C:VAL419 3.7 20.9 1.0
O C:HOH1240 3.8 39.7 1.0
CD1 C:LEU405 4.0 32.0 1.0
CB C:PHE415 4.0 41.0 1.0
C06 C:86X1004 4.0 25.9 0.5
C08 C:86X1004 4.0 25.6 0.5
C08 C:86X1004 4.0 25.8 0.5
C06 C:86X1004 4.1 26.5 0.5
O C:HOH1243 4.2 36.0 1.0
CB C:PRO438 4.4 21.4 1.0
C07 C:86X1004 4.5 25.7 0.5
C07 C:86X1004 4.6 26.7 0.5
O C:PHE415 4.7 34.5 1.0
CG C:LEU405 4.7 36.0 1.0
CD C:PRO438 4.7 20.7 1.0
CD2 C:LEU405 4.7 37.0 1.0
CG C:PHE415 4.8 41.2 1.0
C C:PHE415 4.8 42.0 1.0
CD2 C:PHE415 5.0 39.1 1.0

Chlorine binding site 9 out of 15 in 5xii

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Chlorine binding site 9 out of 15 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl1005

b:68.9
occ:1.00
 O C:GLU376 3.9 27.5 1.0
NZ C:LYS377 4.2 38.0 1.0
CB C:ARG380 4.2 27.1 1.0
C C:GLU376 4.2 26.5 1.0
CD C:LYS377 4.3 36.1 1.0
NH2 C:ARG380 4.3 37.1 1.0
CA C:LYS377 4.4 27.5 1.0
N C:LYS377 4.4 25.9 1.0
CZ C:ARG380 4.4 38.5 1.0
CG C:ARG380 4.5 29.2 1.0
CE C:LYS377 4.5 38.2 1.0
CB C:GLU376 4.5 24.5 1.0
NE C:ARG380 4.5 35.0 1.0
O C:HOH1105 4.7 32.5 1.0
CG C:LYS377 4.7 31.2 1.0
O C:HOH1149 4.9 32.8 1.0
NH1 C:ARG380 4.9 38.3 1.0

Chlorine binding site 10 out of 15 in 5xii

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Chlorine binding site 10 out of 15 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 Chlorine with other atoms in the Cl binding site number 10 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:Cl1004

b:31.6
occ:0.50
 CL4 D:86X1004 0.0 31.6 0.5
CL4 D:86X1004 0.4 32.8 0.5
C03 D:86X1004 1.5 29.1 0.5
C03 D:86X1004 1.7 27.1 0.5
C02 D:86X1004 2.4 27.9 0.5
C05 D:86X1004 2.6 28.0 0.5
F01 D:86X1004 2.6 25.1 0.5
C05 D:86X1004 2.7 25.8 0.5
C02 D:86X1004 2.7 26.2 0.5
F01 D:86X1004 3.0 24.3 0.5
CG D:PRO438 3.6 20.1 1.0
CG2 D:VAL419 3.6 20.5 1.0
C08 D:86X1004 3.7 27.0 0.5
CB D:PHE415 3.8 40.2 1.0
C06 D:86X1004 3.8 27.6 0.5
C06 D:86X1004 4.0 25.3 0.5
C08 D:86X1004 4.0 25.2 0.5
O D:HOH1256 4.1 7.7 0.5
CD1 D:LEU405 4.2 19.5 1.0
C07 D:86X1004 4.3 27.6 0.5
O D:HOH1250 4.3 37.8 1.0
CB D:PRO438 4.5 19.3 1.0
C07 D:86X1004 4.5 25.3 0.5
CG D:PHE415 4.5 37.5 1.0
O D:PHE415 4.7 36.5 1.0
CD D:PRO438 4.7 19.3 1.0
C D:PHE415 4.8 39.8 1.0
CD2 D:LEU405 4.9 19.8 1.0
CD2 D:PHE415 4.9 37.3 1.0
CG D:LEU405 4.9 21.7 1.0
CA D:PHE415 4.9 41.8 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: Fri Jul 26 21:02:44 2024

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