Chlorine in PDB 6p83: E.Coli Lpxd in Complex with Compound 1O

All present enzymatic activity of E.Coli Lpxd in Complex with Compound 1O:
2.3.1.191;

The structure of E.Coli Lpxd in Complex with Compound 1O, PDB code: 6p83 was solved by X.Ma, S.Shia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.63 / 1.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.722, 97.722, 215.999, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 19

The structure of E.Coli Lpxd in Complex with Compound 1O also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the E.Coli Lpxd in Complex with Compound 1O (pdb code 6p83). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the E.Coli Lpxd in Complex with Compound 1O, PDB code: 6p83:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the E.Coli Lpxd in Complex with Compound 1O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of E.Coli Lpxd in Complex with Compound 1O within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:43.9 occ:1.00 CL29 A:O3Y403 0.0 43.9 1.0 C24 A:O3Y403 1.7 30.2 1.0 C25 A:O3Y403 2.7 27.2 1.0 C23 A:O3Y403 2.7 25.7 1.0 H46 A:O3Y403 2.8 32.6 0.0 C4 A:O3Y403 3.1 21.3 1.0 O A:ILE267 3.4 22.5 1.0 C5 A:O3Y403 3.6 25.5 1.0 H42 A:O3Y403 3.6 30.3 0.0 C A:ILE267 3.6 20.6 1.0 N A:ILE267 3.7 20.1 1.0 O14 A:O3Y403 3.8 32.8 1.0 H50 A:O3Y403 3.8 28.5 0.0 C3 A:O3Y403 3.9 21.8 1.0 C6 A:O3Y403 3.9 31.5 1.0 C26 A:O3Y403 3.9 29.7 1.0 C A:MET266 3.9 22.4 1.0 C28 A:O3Y403 3.9 30.8 1.0 CB A:MET266 4.0 24.8 1.0 CB A:ALA250 4.0 22.4 1.0 N A:GLY268 4.0 22.3 1.0 CA A:GLY268 4.1 20.1 1.0 CA A:MET266 4.1 24.6 1.0 O A:ALA248 4.2 21.8 1.0 N A:ALA250 4.3 21.5 1.0 CA A:ILE267 4.3 19.2 1.0 CE A:MET266 4.4 41.1 1.0 C27 A:O3Y403 4.4 30.6 1.0 C13 A:O3Y403 4.4 21.5 1.0 O30 A:O3Y403 4.5 23.7 1.0 C10 A:O3Y403 4.6 26.4 1.0 C21 A:O3Y403 4.6 25.2 1.0 O A:MET266 4.6 22.1 1.0 H41 A:O3Y403 4.7 30.3 0.0 C A:ALA248 4.7 23.8 1.0 CB A:ALA248 4.7 23.6 1.0 CA A:ALA250 4.8 20.4 1.0 H47 A:O3Y403 4.8 35.7 0.0 H49 A:O3Y403 4.8 37.0 0.0 SD A:MET266 4.8 40.0 1.0 C2 A:O3Y403 4.8 20.8 1.0

Chlorine binding site 2 out of 3 in the E.Coli Lpxd in Complex with Compound 1O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of E.Coli Lpxd in Complex with Compound 1O within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl501 b:48.2 occ:1.00 CL29 B:O3Y501 0.0 48.2 1.0 C24 B:O3Y501 1.7 28.8 1.0 C23 B:O3Y501 2.7 27.9 1.0 C25 B:O3Y501 2.7 27.7 1.0 H46 B:O3Y501 2.8 33.3 0.0 C4 B:O3Y501 3.0 26.1 1.0 H42 B:O3Y501 3.3 46.3 0.0 C5 B:O3Y501 3.4 28.4 1.0 O14 B:O3Y501 3.5 36.2 1.0 O B:ILE267 3.6 22.9 1.0 C6 B:O3Y501 3.6 33.3 1.0 C3 B:O3Y501 3.9 26.7 1.0 C26 B:O3Y501 3.9 28.8 1.0 C28 B:O3Y501 3.9 27.0 1.0 N B:ILE267 4.0 20.7 1.0 CB B:ALA250 4.0 19.9 1.0 C B:ILE267 4.0 23.0 1.0 H50 B:O3Y501 4.0 31.3 0.0 CB B:MET266 4.1 24.5 1.0 O B:ALA248 4.1 21.5 1.0 N B:ALA250 4.2 18.1 1.0 CB B:ALA248 4.2 19.8 1.0 C21 B:O3Y501 4.3 38.6 1.0 C B:MET266 4.3 21.2 1.0 CA B:MET266 4.3 23.1 1.0 H40 B:O3Y501 4.4 46.3 0.0 C10 B:O3Y501 4.4 25.8 1.0 C27 B:O3Y501 4.4 32.0 1.0 C B:ALA248 4.5 20.9 1.0 C13 B:O3Y501 4.6 22.9 1.0 N B:GLY268 4.6 20.4 1.0 CA B:GLY268 4.6 22.5 1.0 CA B:ALA250 4.7 20.3 1.0 CA B:ILE267 4.7 20.0 1.0 CG B:MET266 4.7 32.7 1.0 O30 B:O3Y501 4.7 26.1 1.0 C7 B:O3Y501 4.7 34.4 1.0 O B:HOH636 4.7 35.9 1.0 H47 B:O3Y501 4.8 34.6 0.0 H49 B:O3Y501 4.8 32.4 0.0 C2 B:O3Y501 4.8 24.2 1.0 H31 B:O3Y501 4.8 41.3 0.0 N B:VAL249 4.9 20.1 1.0 C B:VAL249 4.9 18.3 1.0 H41 B:O3Y501 4.9 46.3 0.0

Chlorine binding site 3 out of 3 in the E.Coli Lpxd in Complex with Compound 1O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of E.Coli Lpxd in Complex with Compound 1O within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl501 b:43.6 occ:1.00 CL29 C:O3Y501 0.0 43.6 1.0 C24 C:O3Y501 1.7 26.1 1.0 C25 C:O3Y501 2.7 24.7 1.0 C23 C:O3Y501 2.7 25.9 1.0 H46 C:O3Y501 2.8 29.6 0.0 C4 C:O3Y501 3.0 23.6 1.0 H42 C:O3Y501 3.3 38.9 0.0 C5 C:O3Y501 3.4 24.0 1.0 O14 C:O3Y501 3.5 32.2 1.0 C6 C:O3Y501 3.6 31.5 1.0 O C:ILE267 3.7 20.3 1.0 C3 C:O3Y501 3.8 20.6 1.0 CB C:ALA248 3.9 19.0 1.0 CB C:ALA250 3.9 21.7 1.0 C28 C:O3Y501 4.0 28.1 1.0 C26 C:O3Y501 4.0 27.2 1.0 H50 C:O3Y501 4.1 28.4 0.0 N C:ALA250 4.1 17.9 1.0 O C:ALA248 4.1 20.2 1.0 C C:ILE267 4.2 21.4 1.0 N C:ILE267 4.2 18.9 1.0 C C:ALA248 4.3 20.5 1.0 C21 C:O3Y501 4.4 32.4 1.0 C10 C:O3Y501 4.4 24.6 1.0 CA C:ALA250 4.5 16.3 1.0 CB C:MET266 4.5 20.1 1.0 C27 C:O3Y501 4.5 27.9 1.0 C13 C:O3Y501 4.5 20.4 1.0 CA C:MET266 4.6 18.4 1.0 C C:MET266 4.6 20.5 1.0 H41 C:O3Y501 4.6 38.9 0.0 CE2 B:PHE183 4.6 25.2 1.0 N C:VAL249 4.7 16.9 1.0 C C:VAL249 4.7 19.8 1.0 O30 C:O3Y501 4.7 23.7 1.0 N C:GLY268 4.8 21.4 1.0 CA C:GLY268 4.8 17.8 1.0 C7 C:O3Y501 4.8 32.4 1.0 CA C:ALA248 4.8 20.1 1.0 C2 C:O3Y501 4.8 22.6 1.0 H49 C:O3Y501 4.8 33.7 0.0 H47 C:O3Y501 4.8 32.6 0.0 CA C:VAL249 4.9 17.8 1.0 H31 C:O3Y501 4.9 38.8 0.0 CA C:ILE267 4.9 20.9 1.0 H40 C:O3Y501 5.0 38.9 0.0

X.Ma, R.Prathapam, C.Wartchow, B.Chie Leon, C.M.Ho, J.De Vicente, W.Han, M.Li, Y.Lu, S.Ramurthy, S.Shia, M.Steffek, T.Uehara. Structural and Biological Basis of Small Molecule Inhibition of Escherichia Coli Lpxd Acyltransferase Essential For Lipopolysaccharide Biosynthesis. Acs Infect Dis. 2019.
ISSN: ESSN 2373-8227
PubMed: 31402665
DOI: 10.1021/ACSINFECDIS.9B00127