Fluorine in PDB 5u86: Structure of the Aquifex Aeolicus Lpxc/Lpc-069 Complex

All present enzymatic activity of Structure of the Aquifex Aeolicus Lpxc/Lpc-069 Complex:
3.5.1.108;

The structure of Structure of the Aquifex Aeolicus Lpxc/Lpc-069 Complex, PDB code: 5u86 was solved by J.Najeeb, C.-J.Lee, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.53 / 1.62
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	65.990, 65.990, 132.420, 90.00, 90.00, 120.00
R / Rfree (%)	13.9 / 15.4

The structure of Structure of the Aquifex Aeolicus Lpxc/Lpc-069 Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the Structure of the Aquifex Aeolicus Lpxc/Lpc-069 Complex (pdb code 5u86). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of the Aquifex Aeolicus Lpxc/Lpc-069 Complex, PDB code: 5u86:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of the Aquifex Aeolicus Lpxc/Lpc-069 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 Aquifex Aeolicus Lpxc/Lpc-069 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:20.5 occ:0.65 F33 A:81V302 0.0 20.5 0.7 O31 A:81V302 0.8 16.4 0.3 C32 A:81V302 1.3 15.4 0.7 O4 A:PO4304 1.8 21.2 0.5 C30 A:81V302 2.0 14.7 0.3 F34 A:81V302 2.1 19.5 0.7 C30 A:81V302 2.3 14.4 0.7 O A:HOH665 2.5 25.6 0.8 C25 A:81V302 2.6 12.5 0.3 C25 A:81V302 2.7 12.4 0.7 O2 A:PO4304 2.7 27.8 0.5 O31 A:81V302 2.7 16.2 0.7 P A:PO4304 2.8 25.2 0.5 C35 A:81V302 2.8 15.6 0.3 N28 A:81V302 3.1 11.9 0.3 C26 A:81V302 3.2 11.3 0.7 N28 A:81V302 3.2 12.3 0.7 C32 A:81V302 3.2 15.4 0.3 NE2 A:HIS253 3.3 12.8 1.0 C26 A:81V302 3.3 11.4 0.3 O A:HOH593 3.5 14.7 1.0 CD2 A:HIS253 3.5 13.0 1.0 F34 A:81V302 3.6 16.7 0.3 C35 A:81V302 3.6 16.2 0.7 O3 A:PO4304 3.7 31.6 0.5 O A:HOH596 3.9 26.8 0.8 O1 A:PO4304 3.9 26.4 0.5 N24 A:81V302 3.9 13.0 0.3 OD2 A:ASP230 4.0 9.2 1.0 NZ A:LYS227 4.0 27.6 1.0 N24 A:81V302 4.1 12.3 0.7 O27 A:81V302 4.1 9.4 0.7 CE1 A:HIS253 4.2 11.6 1.0 O29 A:81V302 4.3 9.2 0.7 O A:HIS58 4.3 15.9 1.0 F33 A:81V302 4.3 15.3 0.3 O01 A:81V302 4.3 19.1 0.3 O29 A:81V302 4.3 10.2 0.3 O27 A:81V302 4.4 10.8 0.3 O01 A:81V302 4.4 20.0 0.7 CA A:HIS58 4.5 13.7 1.0 C A:HIS58 4.5 14.3 1.0 C02 A:81V302 4.6 15.6 0.3 CG A:HIS253 4.6 9.7 1.0 O A:HOH701 4.7 38.6 1.0 C02 A:81V302 4.7 15.8 0.7 O A:HOH726 4.8 35.6 1.0 CE A:LYS227 4.8 25.4 1.0 ND1 A:HIS253 4.9 10.7 1.0 CD A:LYS227 5.0 18.5 1.0

Fluorine binding site 2 out of 4 in the Structure of the Aquifex Aeolicus Lpxc/Lpc-069 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 Aquifex Aeolicus Lpxc/Lpc-069 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:15.3 occ:0.35 F33 A:81V302 0.0 15.3 0.3 C35 A:81V302 0.9 16.2 0.7 C32 A:81V302 1.3 15.4 0.3 F34 A:81V302 2.2 16.7 0.3 C30 A:81V302 2.3 14.4 0.7 C30 A:81V302 2.4 14.7 0.3 C35 A:81V302 2.8 15.6 0.3 O27 A:81V302 2.8 9.4 0.7 N24 A:81V302 2.9 13.0 0.3 C25 A:81V302 2.9 12.5 0.3 C25 A:81V302 2.9 12.4 0.7 N24 A:81V302 3.1 12.3 0.7 OG1 A:THR179 3.1 10.2 1.0 O27 A:81V302 3.1 10.8 0.3 C32 A:81V302 3.1 15.4 0.7 C26 A:81V302 3.2 11.3 0.7 O31 A:81V302 3.2 16.2 0.7 C26 A:81V302 3.3 11.4 0.3 N A:PHE180 3.4 9.6 1.0 CD1 A:PHE180 3.5 10.4 1.0 CE1 A:PHE180 3.5 10.7 1.0 O A:PHE180 3.5 10.8 1.0 F34 A:81V302 3.6 19.5 0.7 O31 A:81V302 3.6 16.4 0.3 CD2 A:HIS226 3.7 7.4 1.0 CA A:THR179 3.9 6.5 1.0 CG A:PHE180 4.0 11.6 1.0 CZ A:PHE180 4.0 12.1 1.0 CB A:THR179 4.1 8.7 1.0 C A:THR179 4.2 7.3 1.0 C02 A:81V302 4.2 15.6 0.3 NE2 A:HIS226 4.2 6.2 1.0 C02 A:81V302 4.3 15.8 0.7 C A:PHE180 4.3 9.2 1.0 CA A:PHE180 4.3 8.9 1.0 F33 A:81V302 4.3 20.5 0.7 N28 A:81V302 4.4 11.9 0.3 N28 A:81V302 4.5 12.3 0.7 OD2 A:ASP230 4.5 9.2 1.0 ZN A:ZN301 4.5 9.7 1.0 CD2 A:PHE180 4.5 11.4 1.0 O A:HOH461 4.5 23.5 1.0 CE2 A:PHE180 4.5 10.7 1.0 CG A:HIS226 4.7 7.5 1.0 CB A:PHE180 4.7 9.5 1.0 C23 A:81V302 4.8 13.2 0.3 C03 A:81V302 4.9 14.1 0.3

Fluorine binding site 3 out of 4 in the Structure of the Aquifex Aeolicus Lpxc/Lpc-069 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 Aquifex Aeolicus Lpxc/Lpc-069 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:19.5 occ:0.65 F34 A:81V302 0.0 19.5 0.7 C32 A:81V302 1.3 15.4 0.7 O31 A:81V302 1.5 16.4 0.3 F34 A:81V302 2.0 16.7 0.3 C30 A:81V302 2.1 14.7 0.3 F33 A:81V302 2.1 20.5 0.7 C30 A:81V302 2.3 14.4 0.7 C35 A:81V302 2.3 15.6 0.3 C32 A:81V302 2.4 15.4 0.3 NZ A:LYS227 2.6 27.6 1.0 O31 A:81V302 2.7 16.2 0.7 C35 A:81V302 2.8 16.2 0.7 CE A:LYS227 2.9 25.4 1.0 O A:HOH701 3.3 38.6 1.0 CD A:LYS227 3.3 18.5 1.0 O4 A:PO4304 3.3 21.2 0.5 O A:HOH665 3.4 25.6 0.8 O A:HOH593 3.5 14.7 1.0 C25 A:81V302 3.5 12.5 0.3 F33 A:81V302 3.6 15.3 0.3 C25 A:81V302 3.6 12.4 0.7 O2 A:PO4304 3.7 27.8 0.5 P A:PO4304 3.9 25.2 0.5 OD2 A:ASP230 4.0 9.2 1.0 C26 A:81V302 4.1 11.3 0.7 O3 A:PO4304 4.2 31.6 0.5 C26 A:81V302 4.2 11.4 0.3 N24 A:81V302 4.5 13.0 0.3 N28 A:81V302 4.5 11.9 0.3 CG A:LYS227 4.6 11.7 1.0 O27 A:81V302 4.6 9.4 0.7 N28 A:81V302 4.6 12.3 0.7 CZ A:PHE180 4.6 12.1 1.0 N24 A:81V302 4.7 12.3 0.7 CE1 A:PHE180 4.9 10.7 1.0 O A:HOH798 5.0 29.5 1.0 O27 A:81V302 5.0 10.8 0.3

Fluorine binding site 4 out of 4 in the Structure of the Aquifex Aeolicus Lpxc/Lpc-069 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Aquifex Aeolicus Lpxc/Lpc-069 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:16.7 occ:0.35 F34 A:81V302 0.0 16.7 0.3 C32 A:81V302 1.3 15.4 0.3 C35 A:81V302 1.8 16.2 0.7 F34 A:81V302 2.0 19.5 0.7 F33 A:81V302 2.2 15.3 0.3 C32 A:81V302 2.3 15.4 0.7 C30 A:81V302 2.3 14.7 0.3 C30 A:81V302 2.5 14.4 0.7 O31 A:81V302 2.8 16.4 0.3 C35 A:81V302 2.8 15.6 0.3 CE1 A:PHE180 3.1 10.7 1.0 CD A:LYS227 3.2 18.5 1.0 CZ A:PHE180 3.3 12.1 1.0 O31 A:81V302 3.3 16.2 0.7 CE A:LYS227 3.3 25.4 1.0 F33 A:81V302 3.6 20.5 0.7 C25 A:81V302 3.7 12.5 0.3 C25 A:81V302 3.8 12.4 0.7 OD2 A:ASP230 3.8 9.2 1.0 NZ A:LYS227 3.9 27.6 1.0 CD1 A:PHE180 3.9 10.4 1.0 CG A:LYS227 3.9 11.7 1.0 O27 A:81V302 3.9 9.4 0.7 C26 A:81V302 4.0 11.3 0.7 C26 A:81V302 4.1 11.4 0.3 CD2 A:HIS226 4.1 7.4 1.0 CE2 A:PHE180 4.2 10.7 1.0 N24 A:81V302 4.3 13.0 0.3 O27 A:81V302 4.3 10.8 0.3 O A:HOH701 4.4 38.6 1.0 O A:HOH593 4.4 14.7 1.0 N24 A:81V302 4.5 12.3 0.7 CG A:PHE180 4.7 11.6 1.0 N28 A:81V302 4.8 11.9 0.3 CD2 A:PHE180 4.8 11.4 1.0 N28 A:81V302 4.9 12.3 0.7 NE2 A:HIS226 4.9 6.2 1.0 CG A:ASP230 5.0 8.5 1.0

N.Lemaitre, X.Liang, J.Najeeb, C.J.Lee, M.Titecat, E.Leteurtre, M.Simonet, E.J.Toone, P.Zhou, F.Sebbane. Curative Treatment of Severe Gram-Negative Bacterial Infections By A New Class of Antibiotics Targeting Lpxc. Mbio V. 8 2017.
ISSN: ESSN 2150-7511
PubMed: 28743813
DOI: 10.1128/MBIO.00674-17