Fluorine in PDB 6pj3: Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex

All present enzymatic activity of Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex:
3.6.1.54;

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex, PDB code: 6pj3 was solved by J.Cho, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.81 / 2.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.800, 105.800, 53.440, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 21.5

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex (pdb code 6pj3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex, PDB code: 6pj3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex


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 the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:46.2 occ:1.00 F30 A:OKY303 0.0 46.2 1.0 C29 A:OKY303 1.4 43.8 1.0 F32 A:OKY303 2.3 53.7 1.0 F31 A:OKY303 2.3 56.9 1.0 C25 A:OKY303 2.3 44.8 1.0 C24 A:OKY303 2.7 35.5 1.0 CG2 A:ILE152 3.4 32.5 1.0 C26 A:OKY303 3.6 39.1 1.0 CD1 A:PHE141 3.9 26.9 1.0 CE1 A:PHE141 4.1 29.8 1.0 C02 A:OKY303 4.1 37.2 1.0 SD A:MET156 4.1 44.0 1.0 CD1 A:ILE152 4.5 31.5 1.0 C27 A:OKY303 4.7 38.3 1.0 CB A:ILE152 4.7 39.5 1.0 C01 A:OKY303 4.9 39.4 1.0 C08 A:OKY303 4.9 32.5 1.0 CG1 A:ILE152 5.0 37.9 1.0 N03 A:OKY303 5.0 38.3 1.0 CG A:PHE141 5.0 35.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex


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 the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:56.9 occ:1.00 F31 A:OKY303 0.0 56.9 1.0 C29 A:OKY303 1.4 43.8 1.0 F32 A:OKY303 2.2 53.7 1.0 F30 A:OKY303 2.3 46.2 1.0 C25 A:OKY303 2.3 44.8 1.0 C26 A:OKY303 2.7 39.1 1.0 C24 A:OKY303 3.5 35.5 1.0 C27 A:OKY303 4.0 38.3 1.0 CD1 A:PHE141 4.2 26.9 1.0 CG2 A:ILE137 4.4 32.1 1.0 C02 A:OKY303 4.7 37.2 1.0 CB A:PHE141 4.7 33.7 1.0 C01 A:OKY303 4.9 39.4 1.0 CG A:PHE141 4.9 35.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:53.7 occ:1.00 F32 A:OKY303 0.0 53.7 1.0 C29 A:OKY303 1.4 43.8 1.0 F31 A:OKY303 2.2 56.9 1.0 F30 A:OKY303 2.3 46.2 1.0 C25 A:OKY303 2.3 44.8 1.0 C24 A:OKY303 3.1 35.5 1.0 C26 A:OKY303 3.2 39.1 1.0 C02 A:OKY303 4.3 37.2 1.0 SD A:MET156 4.4 44.0 1.0 C27 A:OKY303 4.4 38.3 1.0 C01 A:OKY303 4.8 39.4 1.0 CE A:MET156 4.8 47.6 1.0 CG1 A:VAL132 5.0 40.1 1.0

J.Cho, M.Lee, C.Cochrane, C.Webster, B.Fenton, J.Zhao, J.Hong, P.Zhao. Structural Basis of the Udp-Diacylglucosamine Pyrophosphohydrolase Lpxh Inhibition By Sulfonyl Piperazine Antibiotics Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1912876117