Chlorine in PDB 5j58: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856):
6.1.1.10;

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856), PDB code: 5j58 was solved by X.Barros-Alvarez, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.70 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.970, 106.030, 207.310, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23

The binding sites of Chlorine atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856) (pdb code 5j58). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856), PDB code: 5j58:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl803 b:46.4 occ:1.00 CL2 B:N56803 0.0 46.4 1.0 C16 B:N56803 1.7 41.3 1.0 C17 B:N56803 2.7 40.1 1.0 C15 B:N56803 2.7 42.0 1.0 CE3 B:TRP474 3.1 34.6 1.0 CZ3 B:TRP474 3.4 33.0 1.0 CB B:PHE522 3.8 34.3 1.0 O B:VAL473 3.9 29.9 1.0 CG B:PHE522 3.9 32.6 1.0 C B:N56803 4.0 39.9 1.0 CD2 B:PHE522 4.0 32.2 1.0 C2 B:N56803 4.0 41.3 1.0 CG B:LEU478 4.0 30.3 1.0 CG2 B:VAL473 4.0 36.4 1.0 CD1 B:LEU478 4.1 30.1 1.0 CA B:TRP474 4.2 32.1 1.0 CD2 B:TRP474 4.3 34.2 1.0 C B:VAL473 4.3 32.2 1.0 C1 B:N56803 4.5 40.0 1.0 N B:TRP474 4.5 31.9 1.0 CD2 B:LEU478 4.6 31.2 1.0 CG1 B:VAL473 4.6 34.8 1.0 O B:TRP474 4.7 32.4 1.0 CH2 B:TRP474 4.7 32.8 1.0 CD1 B:PHE522 4.7 31.8 1.0 CE2 B:PHE522 4.8 30.9 1.0 CB B:VAL473 4.8 35.0 1.0 CB B:ALA477 4.9 32.5 1.0 C B:TRP474 5.0 32.0 1.0 CB B:TRP474 5.0 32.3 1.0

Chlorine binding site 2 out of 3 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl803 b:41.7 occ:1.00 CL B:N56803 0.0 41.7 1.0 C B:N56803 1.7 39.9 1.0 C1 B:N56803 2.7 40.0 1.0 C17 B:N56803 2.7 40.1 1.0 CE1 B:HIS523 3.7 26.6 1.0 NE2 B:HIS523 3.7 26.7 1.0 OH B:TYR481 3.8 21.2 1.0 CG1 B:ILE248 3.9 29.4 1.0 N B:ILE248 3.9 29.0 1.0 C16 B:N56803 4.0 41.3 1.0 C2 B:N56803 4.0 41.3 1.0 O B:ILE248 4.3 26.3 1.0 CB B:PRO247 4.3 29.6 1.0 CA B:PRO247 4.4 29.7 1.0 C15 B:N56803 4.5 42.0 1.0 CZ B:TYR481 4.5 22.9 1.0 CB B:ALA477 4.5 32.5 1.0 ND2 B:ASN480 4.6 26.5 1.0 C B:PRO247 4.7 29.1 1.0 CD1 B:ILE519 4.7 34.2 1.0 CD2 B:LEU478 4.7 31.2 1.0 C B:ALA477 4.7 30.4 1.0 O B:ALA477 4.8 31.1 1.0 CD1 B:ILE248 4.8 30.5 1.0 CA B:ILE248 4.8 28.5 1.0 N B:LEU478 4.8 29.0 1.0 CE2 B:TYR481 4.8 24.4 1.0 CB B:ILE248 5.0 28.8 1.0 CA B:LEU478 5.0 28.9 1.0 ND1 B:HIS523 5.0 27.0 1.0

Chlorine binding site 3 out of 3 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1856) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl803 b:40.4 occ:1.00 CL1 B:N56803 0.0 40.4 1.0 C11 B:N56803 1.7 37.2 1.0 N3 B:N56803 2.6 38.4 1.0 C12 B:N56803 2.7 36.3 1.0 O B:VAL471 3.6 30.9 1.0 CD1 B:TYR472 3.8 33.8 1.0 CA B:GLY290 3.8 36.8 1.0 O B:HOH978 3.8 28.1 1.0 C10 B:N56803 3.8 37.8 1.0 N B:VAL473 3.9 32.3 1.0 CD1 B:LEU456 3.9 47.1 1.0 O B:HOH941 3.9 33.2 1.0 C13 B:N56803 4.0 37.1 1.0 CA B:TYR472 4.0 32.5 1.0 C B:TYR472 4.0 32.3 1.0 N B:GLY290 4.1 33.8 1.0 CD2 B:LEU456 4.2 47.0 1.0 CB B:ALA460 4.2 32.3 1.0 CE1 B:TYR472 4.3 34.5 1.0 C14 B:N56803 4.4 37.1 1.0 CA B:VAL473 4.5 33.2 1.0 C B:VAL471 4.6 31.9 1.0 CB B:HIS289 4.6 32.1 1.0 C B:HIS289 4.6 32.4 1.0 CG B:LEU456 4.7 47.0 1.0 O B:TYR472 4.7 32.2 1.0 CG B:TYR472 4.8 33.6 1.0 N B:TYR472 4.8 32.1 1.0 CB B:TYR472 4.9 33.5 1.0 O B:TRP459 5.0 31.6 1.0

W.Huang, Z.Zhang, X.Barros-Alvarez, C.Y.Koh, R.M.Ranade, J.R.Gillespie, S.A.Creason, S.Shibata, C.L.Verlinde, W.G.Hol, F.S.Buckner, E.Fan. Structure-Guided Design of Novel Trypanosoma Brucei Methionyl-Trna Synthetase Inhibitors. Eur J Med Chem V. 124 1081 2016.
ISSN: ISSN 1768-3254
PubMed: 27788467
DOI: 10.1016/J.EJMECH.2016.10.024