Fluorine in PDB 6pib: Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex

All present enzymatic activity of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex:
3.6.1.54;

The structure of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex, PDB code: 6pib 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)	45.96 / 2.26
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.750, 106.750, 52.970, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.9

The structure of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex (pdb code 6pib). 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 the Klebsiella Pneumoniae Lpxh-AZ1 Complex, PDB code: 6pib:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:60.8 occ:1.00 F29 A:OKV303 0.0 60.8 1.0 C28 A:OKV303 1.3 58.6 1.0 F31 A:OKV303 2.2 57.9 1.0 F30 A:OKV303 2.2 66.4 1.0 C25 A:OKV303 2.3 53.6 1.0 C24 A:OKV303 3.1 51.1 1.0 C26 A:OKV303 3.3 54.7 1.0 SD A:MET156 4.0 57.4 1.0 CE A:MET156 4.1 55.1 1.0 C02 A:OKV303 4.3 50.6 1.0 CG2 A:ILE137 4.4 56.5 1.0 CG1 A:VAL132 4.5 49.9 1.0 C27 A:OKV303 4.5 55.7 1.0 C01 A:OKV303 4.9 50.7 1.0

Fluorine binding site 2 out of 3 in the Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:66.4 occ:1.00 F30 A:OKV303 0.0 66.4 1.0 C28 A:OKV303 1.3 58.6 1.0 F31 A:OKV303 2.2 57.9 1.0 F29 A:OKV303 2.2 60.8 1.0 C25 A:OKV303 2.3 53.6 1.0 C26 A:OKV303 2.7 54.7 1.0 CG2 A:ILE137 3.4 56.5 1.0 C24 A:OKV303 3.6 51.1 1.0 O A:ILE137 4.0 56.5 1.0 CB A:PHE141 4.0 52.3 1.0 C27 A:OKV303 4.1 55.7 1.0 CD1 A:PHE141 4.2 45.8 1.0 CG A:PHE141 4.5 48.7 1.0 C02 A:OKV303 4.7 50.6 1.0 C A:ILE137 4.8 59.4 1.0 CB A:ILE137 4.8 59.6 1.0 CA A:PHE141 4.9 53.0 1.0 C01 A:OKV303 4.9 50.7 1.0

Fluorine binding site 3 out of 3 in the Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:57.9 occ:1.00 F31 A:OKV303 0.0 57.9 1.0 C28 A:OKV303 1.3 58.6 1.0 F29 A:OKV303 2.2 60.8 1.0 F30 A:OKV303 2.2 66.4 1.0 C25 A:OKV303 2.3 53.6 1.0 C24 A:OKV303 2.8 51.1 1.0 CD1 A:PHE141 3.4 45.8 1.0 CG2 A:ILE152 3.5 42.8 1.0 C26 A:OKV303 3.5 54.7 1.0 SD A:MET156 3.9 57.4 1.0 CE1 A:PHE141 4.0 47.9 1.0 C02 A:OKV303 4.1 50.6 1.0 CG A:PHE141 4.3 48.7 1.0 CB A:PHE141 4.5 52.3 1.0 CD1 A:ILE152 4.5 49.9 1.0 C27 A:OKV303 4.7 55.7 1.0 CB A:ILE152 4.8 50.3 1.0 CE A:MET156 4.8 55.1 1.0 C04 A:OKV303 4.9 47.4 1.0 C01 A:OKV303 4.9 50.7 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