Fluorine in PDB 7qi8: Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor

All present enzymatic activity of Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor:
6.1.1.6;

The structure of Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor, PDB code: 7qi8 was solved by A.Dawson, D.A.Robinson, J.Tamjar, P.Wyatt, S.Green, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.43 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.196, 84.196, 147.984, 90, 90, 90
R / Rfree (%)	24.4 / 30.5

The binding sites of Fluorine atom in the Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor (pdb code 7qi8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor, PDB code: 7qi8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:80.4 occ:1.00 F1 A:DD0602 0.0 80.4 1.0 C14 A:DD0602 1.4 80.8 1.0 F2 A:DD0602 2.2 85.6 1.0 C13 A:DD0602 2.3 78.7 1.0 C8 A:DD0602 2.3 79.2 1.0 N3 A:DD0602 2.9 75.8 1.0 C6 A:DD0602 3.3 71.6 1.0 N A:GLY478 3.4 42.2 1.0 O2 A:DD0602 3.4 70.1 1.0 SD A:MET271 3.6 75.9 1.0 CA A:GLY478 3.6 44.3 1.0 C A:MET477 3.6 43.2 1.0 C12 A:DD0602 3.7 79.8 1.0 C9 A:DD0602 3.7 76.5 1.0 CE2 A:PHE269 3.8 49.5 1.0 C7 A:DD0602 3.9 71.1 1.0 CE A:MET271 3.9 64.9 1.0 O A:MET477 4.0 41.5 1.0 CG A:MET271 4.1 60.5 1.0 O3 A:DD0602 4.2 68.9 1.0 CA A:MET477 4.3 42.0 1.0 C10 A:DD0602 4.3 74.7 1.0 CZ A:PHE269 4.4 52.8 1.0 C5 A:DD0602 4.4 69.2 1.0 N A:MET477 4.4 39.0 1.0 CB A:MET271 4.4 49.7 1.0 C11 A:DD0602 4.6 79.0 1.0 C4 A:DD0602 4.6 72.4 1.0 NH1 A:ARG257 4.8 68.6 1.0 CD2 A:PHE269 4.8 49.4 1.0 O A:HOH720 5.0 45.0 1.0 C A:GLY476 5.0 36.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Lysyl-Trna Synthetase From Mycobacterium Tuberculosis Complexed with L-Lysine and Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:85.6 occ:1.00 F2 A:DD0602 0.0 85.6 1.0 C14 A:DD0602 1.4 80.8 1.0 F1 A:DD0602 2.2 80.4 1.0 C13 A:DD0602 2.4 78.7 1.0 C8 A:DD0602 2.4 79.2 1.0 O3 A:DD0602 2.9 68.9 1.0 N3 A:DD0602 2.9 75.8 1.0 C12 A:DD0602 2.9 79.8 1.0 C7 A:DD0602 3.1 71.1 1.0 C9 A:DD0602 3.1 76.5 1.0 NH1 A:ARG257 3.3 68.6 1.0 O A:LYS601 3.8 68.9 1.0 CE A:MET271 3.8 64.9 1.0 SD A:MET271 3.9 75.9 1.0 OXT A:LYS601 3.9 50.9 1.0 C11 A:DD0602 4.0 79.0 1.0 C6 A:DD0602 4.0 71.6 1.0 C10 A:DD0602 4.0 74.7 1.0 C A:LYS601 4.2 56.8 1.0 C4 A:DD0602 4.3 72.4 1.0 CZ A:ARG257 4.4 62.5 1.0 O2 A:DD0602 4.6 70.1 1.0 C5 A:DD0602 4.7 69.2 1.0 CZ A:PHE269 4.7 52.8 1.0 CE2 A:PHE269 4.8 49.5 1.0 NH2 A:ARG257 4.9 61.2 1.0

S.R.Green, S.H.Davis, S.Damerow, C.A.Engelhart, M.Mathieson, B.Baragana, D.A.Robinson, J.Tamjar, A.Dawson, F.K.Tamaki, K.I.Buchanan, J.Post, K.Dowers, S.M.Shepherd, C.Jansen, F.Zuccotto, I.H.Gilbert, O.Epemolu, J.Riley, L.Stojanovski, M.Osuna-Cabello, E.Perez-Herran, M.J.Rebollo, L.Guijarro Lopez, P.Casado Castro, I.Camino, H.C.Kim, J.M.Bean, N.Nahiyaan, K.Y.Rhee, Q.Wang, V.Y.Tan, H.I.M.Boshoff, P.J.Converse, S.Y.Li, Y.S.Chang, N.Fotouhi, A.M.Upton, E.L.Nuermberger, D.Schnappinger, K.D.Read, L.Encinas, R.H.Bates, P.G.Wyatt, L.A.T.Cleghorn. Lysyl-Trna Synthetase, A Target For Urgently Needed M. Tuberculosis Drugs. Nat Commun V. 13 5992 2022.
ISSN: ESSN 2041-1723
PubMed: 36220877
DOI: 10.1038/S41467-022-33736-5