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Bromine in PDB 5xiq: Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone

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

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

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone, PDB code: 5xiq 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) 40.32 / 2.19
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.852, 90.898, 92.869, 89.86, 80.92, 75.82
R / Rfree (%) 16.5 / 20.7

Other elements in 5xiq:

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

Magnesium (Mg) 8 atoms
Chlorine (Cl) 4 atoms

Bromine Binding Sites:

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

Bromine binding site 1 out of 4 in 5xiq

Go back to Bromine Binding Sites List in 5xiq
Bromine binding site 1 out of 4 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1002

b:59.7
occ:1.00
 BR1 A:HFG1002 0.0 59.7 1.0
C7 A:HFG1002 1.9 42.4 1.0
C8 A:HFG1002 2.8 35.8 1.0
C6 A:HFG1002 2.8 42.5 1.0
CL1 A:HFG1002 3.2 46.1 1.0
CG2 A:VAL419 3.3 36.0 1.0
O A:PHE415 3.5 48.5 1.0
CB A:PRO438 3.7 31.7 1.0
CB A:GLU418 3.9 36.8 1.0
CG A:PRO438 4.0 33.2 1.0
N A:VAL419 4.0 31.1 1.0
CB A:PHE415 4.1 80.9 1.0
C9 A:HFG1002 4.1 37.2 1.0
C5 A:HFG1002 4.1 37.8 1.0
C A:PHE415 4.2 64.5 1.0
C A:GLU418 4.2 32.2 1.0
OE1 A:GLU418 4.3 38.2 1.0
CA A:VAL419 4.4 30.6 1.0
CB A:VAL419 4.4 32.9 1.0
CA A:PHE415 4.5 72.5 1.0
CA A:GLU418 4.6 35.5 1.0
C10 A:HFG1002 4.6 35.1 1.0
O A:GLU418 4.7 34.1 1.0
CG A:PHE415 4.7 87.1 1.0
N A:GLU418 5.0 38.9 1.0

Bromine binding site 2 out of 4 in 5xiq

Go back to Bromine Binding Sites List in 5xiq
Bromine binding site 2 out of 4 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1002

b:66.3
occ:1.00
 BR1 B:HFG1002 0.0 66.3 1.0
C7 B:HFG1002 1.9 39.7 1.0
C8 B:HFG1002 2.8 34.3 1.0
C6 B:HFG1002 2.8 34.1 1.0
CL1 B:HFG1002 3.2 55.0 1.0
O B:PHE415 3.4 36.2 0.5
CG2 B:VAL419 3.4 38.1 1.0
CB B:PRO438 3.7 33.8 1.0
CB B:GLU418 3.8 47.8 1.0
C B:PHE415 4.0 44.3 0.5
CG B:PRO438 4.1 34.4 1.0
N B:VAL419 4.1 31.7 1.0
C9 B:HFG1002 4.1 34.3 1.0
CB B:PHE415 4.1 44.2 0.5
C5 B:HFG1002 4.1 31.0 1.0
C B:GLU418 4.2 37.5 1.0
OE1 B:GLU418 4.3 40.1 1.0
CA B:VAL419 4.3 35.6 1.0
CB B:VAL419 4.5 35.8 1.0
CA B:PHE415 4.5 45.8 0.5
CA B:GLU418 4.5 41.4 1.0
C10 B:HFG1002 4.6 35.2 1.0
O B:GLU418 4.7 35.8 1.0
CG B:PHE415 4.7 44.2 0.5
N B:SER416 4.8 52.6 1.0
N B:GLU418 4.9 36.8 1.0
CG B:ARG470 5.0 34.7 1.0

Bromine binding site 3 out of 4 in 5xiq

Go back to Bromine Binding Sites List in 5xiq
Bromine binding site 3 out of 4 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br1002

b:64.9
occ:1.00
 BR1 C:HFG1002 0.0 64.9 1.0
C7 C:HFG1002 1.9 43.0 1.0
C8 C:HFG1002 2.8 32.4 1.0
C6 C:HFG1002 2.8 37.0 1.0
CL1 C:HFG1002 3.2 45.4 1.0
CG2 C:VAL419 3.3 34.2 1.0
O C:PHE415 3.3 55.7 1.0
CB C:GLU418 3.7 38.9 1.0
CB C:PRO438 3.7 38.3 1.0
C C:PHE415 3.9 74.8 1.0
CG C:PRO438 4.0 35.2 1.0
N C:VAL419 4.0 35.6 1.0
CB C:PHE415 4.0 87.5 1.0
C C:GLU418 4.1 33.4 1.0
OE1 C:GLU418 4.1 43.6 1.0
C9 C:HFG1002 4.1 35.8 1.0
C5 C:HFG1002 4.1 32.0 1.0
CA C:VAL419 4.3 35.7 1.0
CA C:PHE415 4.3 88.8 1.0
CA C:GLU418 4.4 41.2 1.0
CB C:VAL419 4.4 33.6 1.0
O C:GLU418 4.4 33.2 1.0
C10 C:HFG1002 4.7 33.3 1.0
CG C:PHE415 4.7 85.1 1.0
CG C:GLU418 4.7 41.2 1.0
N C:GLU418 4.8 38.3 1.0
N C:SER416 4.8 65.3 1.0
CD C:GLU418 4.9 42.2 1.0

Bromine binding site 4 out of 4 in 5xiq

Go back to Bromine Binding Sites List in 5xiq
Bromine binding site 4 out of 4 in the Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Toxoplasma Gondii Prolyl-Trna Synthetase (Tgprs) in Complex with Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br1002

b:67.0
occ:1.00
 BR1 D:HFG1002 0.0 67.0 1.0
C7 D:HFG1002 1.9 40.8 1.0
C6 D:HFG1002 2.8 38.0 1.0
C8 D:HFG1002 2.8 33.3 1.0
CL1 D:HFG1002 3.1 58.4 1.0
CG2 D:VAL419 3.4 37.1 1.0
O D:PHE415 3.5 61.6 1.0
CB D:PRO438 3.6 31.0 1.0
CB D:GLU418 3.8 33.9 1.0
CG D:PRO438 3.9 35.3 1.0
CB D:PHE415 3.9 81.9 1.0
C D:PHE415 4.0 73.8 1.0
C5 D:HFG1002 4.1 36.3 1.0
C9 D:HFG1002 4.1 31.0 1.0
N D:VAL419 4.3 36.9 1.0
C D:GLU418 4.3 31.6 1.0
CA D:PHE415 4.4 86.9 1.0
OE1 D:GLU418 4.5 36.1 1.0
CG D:PHE415 4.5 80.0 1.0
CA D:VAL419 4.6 34.4 1.0
CA D:GLU418 4.6 35.0 1.0
C10 D:HFG1002 4.6 30.9 1.0
CB D:VAL419 4.6 37.3 1.0
O D:GLU418 4.7 34.9 1.0
CG D:GLU418 4.9 35.6 1.0
CD1 D:PHE415 4.9 82.0 1.0
N D:SER416 4.9 62.8 1.0
O D:HOH1175 5.0 53.3 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 Jul 11 01:18:41 2024

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