Fluorine in PDB 8e4a: Pseudomonas Lpxc in Complex with Lpc-233

All present enzymatic activity of Pseudomonas Lpxc in Complex with Lpc-233:
3.5.1.108;

The structure of Pseudomonas Lpxc in Complex with Lpc-233, PDB code: 8e4a was solved by J.Najeeb, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.04 / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.97, 66.45, 63.84, 90, 90.68, 90
R / Rfree (%)	17.2 / 20.5

The structure of Pseudomonas Lpxc in Complex with Lpc-233 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Fluorine atom in the Pseudomonas Lpxc in Complex with Lpc-233 (pdb code 8e4a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pseudomonas Lpxc in Complex with Lpc-233, PDB code: 8e4a:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Pseudomonas Lpxc in Complex with Lpc-233


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pseudomonas Lpxc in Complex with Lpc-233 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:35.6 occ:1.00 F26 A:UFX302 0.0 35.6 1.0 C25 A:UFX302 1.4 23.7 1.0 F27 A:UFX302 2.2 41.2 1.0 C22 A:UFX302 2.4 26.2 1.0 C05 A:UFX302 2.7 19.5 1.0 O23 A:UFX302 2.9 35.6 1.0 C02 A:UFX302 3.0 21.9 1.0 O A:HOH588 3.1 19.9 1.0 O A:HOH537 3.2 22.0 1.0 N03 A:UFX302 3.3 19.2 1.0 NZ A:LYS238 3.6 21.7 1.0 O A:HOH628 3.6 36.8 1.0 C24 A:UFX302 3.7 12.9 1.0 O01 A:UFX302 3.7 18.3 1.0 O A:HOH612 3.9 27.9 1.0 N06 A:UFX302 4.1 16.1 1.0 OD2 A:ASP241 4.1 7.0 1.0 NE2 A:HIS264 4.2 14.3 1.0 O04 A:UFX302 4.3 19.3 1.0 CD A:LYS238 4.6 12.1 1.0 O A:MET62 4.6 24.5 1.0 CE A:LYS238 4.7 21.1 1.0 CD2 A:HIS264 4.7 16.2 1.0 O08 A:UFX302 5.0 25.7 1.0 CE1 A:HIS264 5.0 13.0 1.0

Fluorine binding site 2 out of 2 in the Pseudomonas Lpxc in Complex with Lpc-233


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pseudomonas Lpxc in Complex with Lpc-233 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:41.2 occ:1.00 F27 A:UFX302 0.0 41.2 1.0 C25 A:UFX302 1.4 23.7 1.0 F26 A:UFX302 2.2 35.6 1.0 C22 A:UFX302 2.3 26.2 1.0 O23 A:UFX302 2.6 35.6 1.0 NZ A:LYS238 2.9 21.7 1.0 C24 A:UFX302 3.0 12.9 1.0 CD A:LYS238 3.1 12.1 1.0 CE A:LYS238 3.5 21.1 1.0 C05 A:UFX302 3.7 19.5 1.0 CZ A:PHE191 3.9 18.4 1.0 O A:HOH537 3.9 22.0 1.0 C02 A:UFX302 4.3 21.9 1.0 CE1 A:PHE191 4.3 17.6 1.0 O A:HOH612 4.4 27.9 1.0 CG A:LYS238 4.4 11.2 1.0 CE2 A:PHE191 4.5 22.5 1.0 O01 A:UFX302 4.6 18.3 1.0 O A:HOH588 4.7 19.9 1.0 N06 A:UFX302 4.8 16.1 1.0 OD2 A:ASP241 4.9 7.0 1.0 O A:HOH628 5.0 36.8 1.0

J.Zhao, C.S.Cochrane, J.Najeeb, D.Gooden, C.Sciandra, P.Fan, N.Lemaitre, K.Newns, R.A.Nicholas, Z.Guan, J.T.Thaden, V.G.Fowler Jr., I.Spasojevic, F.Sebbane, E.J.Toone, C.Duncan, R.Gammans, P.Zhou. Preclinical Safety and Efficacy Characterization of An Lpxc Inhibitor Against Gram-Negative Pathogens. Sci Transl Med V. 15 F5668 2023.
ISSN: ESSN 1946-6242
PubMed: 37556556
DOI: 10.1126/SCITRANSLMED.ADF5668