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Chlorine in PDB 5xif: Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii

Enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii

All present enzymatic activity of Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii:
6.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii, PDB code: 5xif 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) 53.41 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.680, 86.430, 97.160, 90.00, 106.46, 90.00
R / Rfree (%) 19.3 / 25

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 7 in 5xif

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Chlorine binding site 1 out of 7 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii


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 Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:69.2
occ:1.00
 CE A:MET601 3.2 51.8 1.0
OH A:TYR830 3.5 41.1 1.0
OG A:SER343 4.1 41.3 1.0
CD1 A:LEU480 4.1 35.7 1.0
CE1 A:TYR830 4.3 39.4 1.0
CE2 A:PHE342 4.4 30.1 1.0
CD2 A:TYR346 4.4 26.9 1.0
CZ A:TYR830 4.4 37.5 1.0
CG2 A:THR477 4.5 42.4 1.0
NH2 A:ARG481 4.5 64.1 1.0
CG A:TYR346 4.6 25.7 1.0
CD2 A:PHE342 4.6 31.7 1.0
CA A:SER343 4.6 33.1 1.0
CB A:TYR346 4.8 25.0 1.0
CB A:SER343 4.9 31.6 1.0
CE2 A:TYR346 4.9 26.3 1.0
SD A:MET601 4.9 42.8 1.0

Chlorine binding site 2 out of 7 in 5xif

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Chlorine binding site 2 out of 7 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii


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 Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl902

b:64.5
occ:1.00
 OG A:SER588 3.7 34.5 1.0
N A:TRP589 3.9 28.2 1.0
CB A:SER588 4.1 29.1 1.0
CH2 A:TRP487 4.1 36.5 1.0
C A:TRP589 4.2 27.4 1.0
CZ3 A:TRP487 4.3 38.7 1.0
O A:TRP589 4.3 26.9 1.0
CA A:TRP589 4.4 26.2 1.0
CD2 A:HIS560 4.5 29.2 1.0
C A:SER588 4.5 31.9 1.0
N A:GLY590 4.5 25.9 1.0
CB A:GLU489 4.6 27.7 1.0
NE2 A:HIS560 4.6 30.4 1.0
CE1 A:HIS491 4.8 30.0 1.0
NE2 A:HIS491 4.8 30.3 1.0
OE1 A:GLU489 4.8 39.6 1.0
CA A:SER588 4.9 30.0 1.0
CA A:GLY590 4.9 26.8 1.0

Chlorine binding site 3 out of 7 in 5xif

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Chlorine binding site 3 out of 7 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii


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 Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl903

b:55.9
occ:0.75
 O A:MET717 4.0 37.2 1.0
C A:MET717 4.0 36.3 1.0
N A:GLU718 4.0 34.7 1.0
CA A:GLU718 4.1 36.8 1.0
CB A:MET717 4.1 35.0 1.0
CB A:PRO613 4.3 29.0 1.0
CG A:GLU718 4.5 57.2 1.0
CB A:GLN721 4.6 30.7 1.0
NE A:ARG614 4.7 56.3 1.0
CA A:MET717 4.8 34.5 1.0
CB A:GLU718 4.9 47.3 1.0
NH2 A:ARG614 4.9 62.4 1.0
N A:ARG614 4.9 31.1 1.0
OE1 A:GLN721 5.0 31.4 1.0

Chlorine binding site 4 out of 7 in 5xif

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Chlorine binding site 4 out of 7 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii


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 Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl901

b:68.9
occ:1.00
 CE B:MET601 3.2 44.8 1.0
OH B:TYR830 3.9 46.5 1.0
CD2 B:TYR346 4.1 36.0 1.0
CG2 B:THR477 4.1 66.8 1.0
CA B:SER343 4.1 45.3 1.0
CB B:SER343 4.2 43.2 1.0
CE2 B:PHE342 4.3 41.1 1.0
CD2 B:PHE342 4.4 38.4 1.0
CG B:TYR346 4.5 39.0 1.0
CE2 B:TYR346 4.5 38.4 1.0
CB B:TYR346 4.7 40.4 1.0
CD1 B:LEU480 4.7 50.4 1.0
N B:SER343 4.8 46.9 1.0
CE2 B:TYR830 4.9 48.2 1.0
CZ B:TYR830 4.9 44.6 1.0
SD B:MET601 4.9 39.7 1.0

Chlorine binding site 5 out of 7 in 5xif

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Chlorine binding site 5 out of 7 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii


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 Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl902

b:47.7
occ:0.55
 NZ B:LYS377 3.6 55.8 1.0
CD B:LYS377 4.0 57.4 1.0
CE B:LYS377 4.1 54.1 1.0
O B:GLU376 4.2 36.2 1.0
C B:GLU376 4.3 33.4 1.0
CA B:LYS377 4.4 37.5 1.0
CB B:ARG380 4.4 35.4 1.0
N B:LYS377 4.5 36.1 1.0
CB B:GLU376 4.5 32.9 1.0
NH2 B:ARG380 4.5 59.1 1.0
CZ B:ARG380 4.6 60.2 1.0
NE B:ARG380 4.6 53.9 1.0
CG B:ARG380 4.7 39.9 1.0
CG B:LYS377 4.9 51.7 1.0
O B:HOH1024 4.9 39.5 1.0

Chlorine binding site 6 out of 7 in 5xif

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Chlorine binding site 6 out of 7 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii


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 Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl903

b:67.3
occ:1.00
 CD B:ARG552 3.7 38.4 1.0
NH1 B:ARG481 3.8 91.1 1.0
NE B:ARG552 3.8 40.8 1.0
NH2 B:ARG481 3.8 91.7 1.0
CZ B:ARG552 4.1 38.9 1.0
CD2 B:TYR830 4.1 44.4 1.0
NH1 B:ARG552 4.2 40.2 1.0
CZ B:ARG481 4.2 93.8 1.0
O B:SER829 4.2 42.4 1.0
CE2 B:TYR830 4.3 48.2 1.0
CA B:TYR830 4.5 45.5 1.0
CG B:TYR830 4.6 47.4 1.0
NH2 B:ARG552 4.8 39.0 1.0
CZ B:TYR830 4.9 44.6 1.0

Chlorine binding site 7 out of 7 in 5xif

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Chlorine binding site 7 out of 7 in the Crystal Structure of Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii


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 Prolyl-Trna Synthetase (Prs) From Toxoplasma Gondii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl904

b:46.8
occ:0.50
 CH2 B:TRP487 4.0 37.8 1.0
OG B:SER588 4.0 45.9 1.0
CZ3 B:TRP487 4.2 37.7 1.0
N B:TRP589 4.3 34.6 1.0
CB B:SER588 4.3 39.8 1.0
C B:TRP589 4.3 34.4 1.0
OE1 B:GLU489 4.3 44.4 1.0
O B:TRP589 4.4 36.5 1.0
CA B:TRP589 4.6 32.3 1.0
N B:GLY590 4.6 33.6 1.0
CD2 B:HIS560 4.7 42.5 1.0
NE2 B:HIS560 4.7 43.0 1.0
CB B:GLU489 4.7 39.4 1.0
C B:SER588 4.8 37.4 1.0
CE1 B:HIS491 4.8 41.8 1.0
OE2 B:GLU441 4.9 59.3 1.0
NE2 B:HIS491 4.9 42.1 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 20:56:47 2024

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