Fluorine in PDB 8qk9: Structure of E. Coli Lpxh in Complex with Jedi-1444

The structure of Structure of E. Coli Lpxh in Complex with Jedi-1444, PDB code: 8qk9 was solved by S.Sooriyaarachchi, T.Bergfors, T.A.Jones, S.L.Mowbray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.309, 81.178, 32.974, 90, 103.32, 90
R / Rfree (%)	17.8 / 21.2

The structure of Structure of E. Coli Lpxh in Complex with Jedi-1444 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the Structure of E. Coli Lpxh in Complex with Jedi-1444 (pdb code 8qk9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of E. Coli Lpxh in Complex with Jedi-1444, PDB code: 8qk9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of E. Coli Lpxh in Complex with Jedi-1444


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of E. Coli Lpxh in Complex with Jedi-1444 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:91.0 occ:1.00 F38 A:VQ9303 0.0 91.0 1.0 C37 A:VQ9303 1.4 68.2 1.0 F40 A:VQ9303 2.2 76.5 1.0 F39 A:VQ9303 2.2 79.5 1.0 C5 A:VQ9303 2.3 54.2 1.0 C6 A:VQ9303 2.8 49.6 1.0 O A:LEU137 2.8 49.1 1.0 CB A:PHE141 3.1 40.5 1.0 CG A:LEU137 3.3 49.4 1.0 C A:LEU137 3.4 52.5 1.0 C4 A:VQ9303 3.5 47.7 1.0 CA A:GLN138 3.7 49.2 1.0 N A:GLN138 3.7 50.2 1.0 CG A:PHE141 3.8 43.3 1.0 CD1 A:LEU137 4.0 53.2 1.0 CD2 A:LEU137 4.1 53.4 1.0 C1 A:VQ9303 4.1 56.0 1.0 CB A:LEU137 4.2 49.8 1.0 CA A:PHE141 4.3 43.6 1.0 N A:PHE141 4.3 43.8 1.0 CA A:LEU137 4.4 48.1 1.0 CD1 A:PHE141 4.4 36.1 1.0 C A:GLN138 4.5 43.1 1.0 O A:GLN138 4.6 43.2 1.0 CD2 A:PHE141 4.6 43.1 1.0 C3 A:VQ9303 4.6 52.5 1.0 CG A:GLN138 4.7 43.4 1.0 CB A:GLN138 4.8 44.6 1.0 C2 A:VQ9303 4.9 52.6 1.0

Fluorine binding site 2 out of 3 in the Structure of E. Coli Lpxh in Complex with Jedi-1444


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of E. Coli Lpxh in Complex with Jedi-1444 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:79.5 occ:1.00 F39 A:VQ9303 0.0 79.5 1.0 C37 A:VQ9303 1.3 68.2 1.0 F40 A:VQ9303 2.1 76.5 1.0 F38 A:VQ9303 2.2 91.0 1.0 C5 A:VQ9303 2.3 54.2 1.0 C4 A:VQ9303 2.6 47.7 1.0 CB A:PHE141 3.5 40.5 1.0 C6 A:VQ9303 3.6 49.6 1.0 CA A:GLN138 3.6 49.2 1.0 CD2 A:LEU83 3.6 36.0 1.0 CG A:PHE141 3.7 43.3 1.0 CD2 A:PHE141 3.7 43.1 1.0 CD1 A:LEU83 3.8 36.8 1.0 CG A:GLN138 3.9 43.4 1.0 C3 A:VQ9303 4.0 52.5 1.0 CG A:LEU83 4.1 37.9 1.0 CB A:GLN138 4.1 44.6 1.0 CE2 A:PHE82 4.3 35.8 1.0 O A:LEU137 4.3 49.1 1.0 N A:GLN138 4.3 50.2 1.0 O A:GLN138 4.4 43.2 1.0 C A:GLN138 4.5 43.1 1.0 CD1 A:PHE141 4.5 36.1 1.0 O A:VAL132 4.5 50.9 1.0 CE2 A:PHE141 4.6 37.0 1.0 C8 A:VQ9303 4.6 45.2 1.0 C A:LEU137 4.6 52.5 1.0 C1 A:VQ9303 4.7 56.0 1.0 CZ A:PHE82 4.8 38.6 1.0 C2 A:VQ9303 4.8 52.6 1.0 N7 A:VQ9303 4.8 48.7 1.0 CA A:PHE141 4.9 43.6 1.0

Fluorine binding site 3 out of 3 in the Structure of E. Coli Lpxh in Complex with Jedi-1444


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of E. Coli Lpxh in Complex with Jedi-1444 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:76.5 occ:1.00 F40 A:VQ9303 0.0 76.5 1.0 C37 A:VQ9303 1.3 68.2 1.0 F39 A:VQ9303 2.1 79.5 1.0 F38 A:VQ9303 2.2 91.0 1.0 C5 A:VQ9303 2.4 54.2 1.0 O A:VAL132 3.2 50.9 1.0 C6 A:VQ9303 3.2 49.6 1.0 CA A:VAL132 3.2 45.8 1.0 C4 A:VQ9303 3.2 47.7 1.0 CB A:VAL132 3.3 42.4 1.0 C A:VAL132 3.6 46.8 1.0 CG1 A:VAL132 3.7 45.6 1.0 CG A:GLN138 3.8 43.4 1.0 CG A:LEU137 4.1 49.4 1.0 CA A:GLN138 4.1 49.2 1.0 N A:GLN138 4.2 50.2 1.0 CE2 A:PHE82 4.2 35.8 1.0 CD2 A:LEU137 4.2 53.4 1.0 C1 A:VQ9303 4.4 56.0 1.0 C A:LEU137 4.4 52.5 1.0 C3 A:VQ9303 4.4 52.5 1.0 O A:LEU137 4.5 49.1 1.0 N A:VAL132 4.5 55.6 1.0 CB A:GLN138 4.5 44.6 1.0 CZ A:PHE82 4.6 38.6 1.0 CB A:LEU137 4.7 49.8 1.0 CG2 A:VAL132 4.7 48.9 1.0 O A:LYS131 4.8 59.6 1.0 C2 A:VQ9303 4.9 52.6 1.0 N A:HIS133 4.9 47.5 1.0 CB A:PHE141 4.9 40.5 1.0 CD A:GLN138 5.0 47.4 1.0 CD2 A:LEU83 5.0 36.0 1.0

D.L.Huseby, S.Cao, E.Zamaratski, S.Sooriyaarachchi, S.Ahmad, T.Bergfors, L.Krasnova, J.Pelss, M.Ikaunieks, E.Loza, M.Katkevics, O.Bobileva, H.Cirule, B.Gukalova, S.Grinberga, M.Backlund, I.Simoff, A.T.Leber, T.Berruga-Fernandez, D.Antonov, V.R.Konda, S.Lindstrom, G.Olanders, P.Brandt, P.Baranczewski, C.Vingsbo Lundberg, E.Liepinsh, E.Suna, T.A.Jones, S.L.Mowbray, D.Hughes, A.Karlen. Antibiotic Class with Potent in Vivo Activity Targeting Lipopolysaccharide Synthesis in Gram-Negative Bacteria. Proc.Natl.Acad.Sci.Usa V. 121 74121 2024.
ISSN: ESSN 1091-6490
PubMed: 38579010
DOI: 10.1073/PNAS.2317274121