Chlorine in PDB 5xih: Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5

Enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5

All present enzymatic activity of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5, PDB code: 5xih 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) 47.06 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.710, 90.763, 93.034, 89.71, 80.58, 75.77
R / Rfree (%) 17.6 / 22.6

Other elements in 5xih:

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5 also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 8 in 5xih

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Chlorine binding site 1 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1005

b:40.0
occ:0.50
 CL A:CL1005 0.0 40.0 0.5
CL A:CL1005 2.4 38.2 0.5
O A:HOH1264 3.1 45.9 1.0
NH2 A:ARG483 3.3 31.7 1.0
NH1 A:ARG483 3.4 30.1 1.0
CZ A:ARG483 3.8 34.2 1.0
NE1 A:TRP471 4.3 26.7 1.0
OH B:TYR425 4.4 33.0 1.0
CD1 A:TRP471 4.4 25.3 1.0
CZ B:TYR425 4.5 35.3 1.0
CE1 B:TYR425 4.9 32.2 1.0
O A:HOH1182 4.9 43.0 1.0
CE2 B:TYR425 5.0 32.7 1.0

Chlorine binding site 2 out of 8 in 5xih

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Chlorine binding site 2 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1005

b:38.2
occ:0.50
 CL A:CL1005 0.0 38.2 0.5
CL A:CL1005 2.4 40.0 0.5
NE1 A:TRP471 3.3 26.7 1.0
NH1 A:ARG483 3.7 30.1 1.0
CD2 B:LEU430 4.0 28.7 1.0
O A:HOH1229 4.1 21.1 0.5
CE1 B:TYR425 4.2 32.2 1.0
CD1 A:TRP471 4.2 25.3 1.0
CE2 A:TRP471 4.4 26.6 1.0
CD B:PRO431 4.4 33.6 1.0
CZ B:TYR425 4.6 35.3 1.0
CD1 B:TYR425 4.6 30.1 1.0
CZ A:ARG483 4.6 34.2 1.0
O A:HOH1148 4.6 46.8 1.0
CZ2 A:TRP471 4.7 27.0 1.0
NH2 A:ARG483 4.7 31.7 1.0
OH B:TYR425 4.8 33.0 1.0
CG B:PRO431 4.8 35.8 1.0

Chlorine binding site 3 out of 8 in 5xih

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Chlorine binding site 3 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1005

b:37.4
occ:0.50
 CA C:SER343 3.4 30.6 1.0
CB C:SER343 3.5 33.3 1.0
O C:HOH1254 3.7 30.5 1.0
N C:SER343 4.1 30.1 1.0
CD2 C:PHE342 4.3 27.9 1.0
CD2 C:TYR346 4.4 22.6 1.0
CB C:TYR346 4.4 22.8 1.0
C C:SER343 4.6 30.9 1.0
CE2 C:PHE342 4.6 28.0 1.0
O C:SER343 4.6 29.2 1.0
CG C:TYR346 4.6 24.4 1.0
C C:PHE342 4.7 31.1 1.0
OH C:TYR830 4.7 25.8 1.0
O C:PHE342 4.8 33.1 1.0
OG C:SER343 4.8 42.0 1.0
CG2 C:THR477 5.0 27.3 1.0

Chlorine binding site 4 out of 8 in 5xih

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Chlorine binding site 4 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1006

b:48.0
occ:0.70
 CL C:CL1006 0.0 48.0 0.7
CL C:CL1006 1.9 36.4 0.3
O C:HOH1277 3.1 43.6 1.0
NE1 C:TRP471 3.1 24.2 1.0
NH1 C:ARG483 3.7 22.8 1.0
CD2 D:LEU430 3.7 26.8 1.0
CD1 C:TRP471 4.0 24.2 1.0
CE1 D:TYR425 4.1 28.0 1.0
CE2 C:TRP471 4.2 22.9 1.0
O C:HOH1231 4.4 13.5 0.5
CD1 D:TYR425 4.5 26.0 1.0
CD D:PRO431 4.5 32.1 1.0
CZ D:TYR425 4.5 29.0 1.0
CZ2 C:TRP471 4.5 23.3 1.0
CZ C:ARG483 4.6 24.6 1.0
O C:HOH1169 4.7 28.0 1.0
NH2 C:ARG483 4.8 24.8 1.0
OH D:TYR425 4.8 32.6 1.0

Chlorine binding site 5 out of 8 in 5xih

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1006

b:36.4
occ:0.30
 CL C:CL1006 0.0 36.4 0.3
CL C:CL1006 1.9 48.0 0.7
O C:HOH1249 3.5 36.6 1.0
NH1 C:ARG483 3.7 22.8 1.0
NH2 C:ARG483 3.8 24.8 1.0
NE1 C:TRP471 4.0 24.2 1.0
OH D:TYR425 4.2 32.6 1.0
CZ D:TYR425 4.2 29.0 1.0
CZ C:ARG483 4.2 24.6 1.0
CD1 C:TRP471 4.4 24.2 1.0
CE1 D:TYR425 4.4 28.0 1.0
CE2 D:TYR425 4.7 27.6 1.0
O C:HOH1277 4.9 43.6 1.0

Chlorine binding site 6 out of 8 in 5xih

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1007

b:56.0
occ:1.00
 NE C:ARG352 3.2 40.0 1.0
NH2 C:ARG352 3.6 38.4 1.0
CB C:VAL351 3.6 25.8 1.0
CG1 C:VAL351 3.6 23.7 1.0
CZ C:ARG352 3.9 39.9 1.0
CA C:GLN348 4.1 26.2 1.0
CG2 C:VAL351 4.1 25.8 1.0
CG C:ARG352 4.2 31.6 1.0
CD C:ARG352 4.3 35.5 1.0
CG C:GLN348 4.3 32.1 1.0
O C:THR347 4.6 24.6 1.0
CB C:GLN348 4.7 28.4 1.0
N C:GLN348 4.7 25.1 1.0
CG2 C:THR347 4.8 24.6 1.0
O C:GLN348 4.9 22.7 1.0
C C:THR347 4.9 25.6 1.0
CA C:VAL351 5.0 24.5 1.0
N C:ARG352 5.0 25.8 1.0

Chlorine binding site 7 out of 8 in 5xih

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Chlorine binding site 7 out of 8 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1005

b:51.9
occ:0.65
 CA D:SER343 3.9 35.4 1.0
OH D:TYR830 3.9 36.3 1.0
OG D:SER343 4.1 45.5 1.0
CB D:SER343 4.4 38.7 1.0
CD2 D:PHE342 4.4 33.7 1.0
CB D:TYR346 4.4 25.3 1.0
N D:SER343 4.4 34.0 1.0
CD2 D:TYR346 4.5 24.1 1.0
CE2 D:PHE342 4.5 33.2 1.0
CG D:TYR346 4.6 26.3 1.0
O D:HOH1236 4.7 26.7 1.0
O D:PHE342 4.8 38.3 1.0
C D:PHE342 4.8 36.9 1.0
CG2 D:THR477 4.9 23.6 1.0
O D:SER343 4.9 32.9 1.0
C D:SER343 4.9 34.1 1.0

Chlorine binding site 8 out of 8 in 5xih

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1006

b:42.4
occ:0.65
 NE D:ARG352 3.3 44.3 1.0
NH2 D:ARG352 3.5 43.8 1.0
CZ D:ARG352 3.8 46.5 1.0
CG1 D:VAL351 4.0 19.7 1.0
CB D:VAL351 4.1 22.6 1.0
CA D:GLN348 4.1 28.5 1.0
O D:HOH1180 4.2 37.6 1.0
CD D:ARG352 4.3 35.1 1.0
CG D:ARG352 4.4 31.4 1.0
CG D:GLN348 4.4 30.7 1.0
O D:THR347 4.6 32.3 1.0
CB D:GLN348 4.6 28.9 1.0
O D:GLN348 4.7 26.0 1.0
CG2 D:VAL351 4.7 19.4 1.0
N D:GLN348 4.9 27.3 1.0
C D:GLN348 4.9 26.9 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 21:02:45 2024

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