Fluorine in PDB 6yku: Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F

All present enzymatic activity of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F:
6.1.1.4;

The structure of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F, PDB code: 6yku was solved by L.Pang, S.V.Strelkov, S.D.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.50 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.109, 80.742, 224.012, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.1

The structure of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F (pdb code 6yku). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F, PDB code: 6yku:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:59.8 occ:1.00 F23 A:OVB1102 0.0 59.8 1.0 C22 A:OVB1102 1.3 57.4 1.0 F24 A:OVB1102 2.1 58.6 1.0 F25 A:OVB1102 2.1 61.8 1.0 O21 A:OVB1102 2.2 53.0 1.0 C18 A:OVB1102 2.8 53.8 1.0 C17 A:OVB1102 2.9 39.3 1.0 N A:LYS637 3.7 51.2 1.0 O A:HOH1487 3.7 50.4 1.0 CA A:SER636 3.7 52.4 1.0 C A:SER636 3.9 50.7 1.0 O A:HOH1256 4.0 56.0 1.0 C19 A:OVB1102 4.1 45.6 1.0 C16 A:OVB1102 4.2 48.3 1.0 N A:SER636 4.2 45.3 1.0 O A:MET635 4.2 42.2 1.0 C A:MET635 4.4 46.6 1.0 CA A:LYS637 4.6 55.9 1.0 O A:SER636 4.7 49.3 1.0 CB A:LYS637 4.9 53.0 1.0

Fluorine binding site 2 out of 3 in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:58.6 occ:1.00 F24 A:OVB1102 0.0 58.6 1.0 C22 A:OVB1102 1.3 57.4 1.0 F23 A:OVB1102 2.1 59.8 1.0 F25 A:OVB1102 2.1 61.8 1.0 O21 A:OVB1102 2.2 53.0 1.0 O A:HOH1522 3.5 55.7 1.0 C18 A:OVB1102 3.5 53.8 1.0 O A:HOH1385 3.7 59.7 1.0 CA A:GLY642 4.1 40.7 1.0 C17 A:OVB1102 4.3 39.3 1.0 C19 A:OVB1102 4.4 45.6 1.0 O A:HOH1318 4.5 35.2 1.0 N A:LYS637 4.6 51.2 1.0 C A:SER636 4.7 50.7 1.0 N A:GLY642 4.8 43.6 1.0 CB A:HIS49 4.8 39.0 1.0 C A:GLY642 4.9 47.8 1.0

Fluorine binding site 3 out of 3 in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11F within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:61.8 occ:1.00 F25 A:OVB1102 0.0 61.8 1.0 C22 A:OVB1102 1.3 57.4 1.0 F24 A:OVB1102 2.1 58.6 1.0 F23 A:OVB1102 2.1 59.8 1.0 O21 A:OVB1102 2.2 53.0 1.0 C18 A:OVB1102 2.7 53.8 1.0 N A:SER636 3.2 45.3 1.0 CA A:GLY642 3.3 40.7 1.0 C A:MET635 3.4 46.6 1.0 C19 A:OVB1102 3.4 45.6 1.0 CA A:SER636 3.5 52.4 1.0 CB A:MET635 3.5 39.0 1.0 C17 A:OVB1102 3.6 39.3 1.0 C A:SER636 3.7 50.7 1.0 O A:MET635 3.7 42.2 1.0 N A:GLY642 3.8 43.6 1.0 CA A:MET635 4.0 48.0 1.0 O A:SER636 4.0 49.3 1.0 N A:LYS637 4.1 51.2 1.0 C20 A:OVB1102 4.5 42.1 1.0 C A:GLY642 4.5 47.8 1.0 O A:HOH1318 4.6 35.2 1.0 C16 A:OVB1102 4.7 48.3 1.0 CG A:MET635 4.7 40.6 1.0 O A:HOH1256 4.8 56.0 1.0 O A:HOH1522 4.8 55.7 1.0 C A:ASN641 4.8 45.3 1.0 O A:HOH1385 4.9 59.7 1.0 SD A:MET635 5.0 39.3 1.0

D.De Ruysscher, L.Pang, S.M.G.Lenders, D.Cappoen, P.Cos, J.Rozenski, S.V.Strelkov, S.D.Weeks, A.Van Aerschot. Synthesis and Structure-Activity Studies of Novel Anhydrohexitol-Based Leucyl-Trna Synthetase Inhibitors. Eur.J.Med.Chem. 13021 2020.
ISSN: ISSN 0223-5234
PubMed: 33248851
DOI: 10.1016/J.EJMECH.2020.113021