Zinc in PDB 5u3b: Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01

All present enzymatic activity of Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01:
3.5.1.108;

The structure of Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01, PDB code: 5u3b was solved by E.R.Sprague, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.59 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.826, 98.432, 165.187, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.3

The binding sites of Zinc atom in the Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01 (pdb code 5u3b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01, PDB code: 5u3b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:19.3 occ:1.00 NE2 A:HIS78 2.0 18.7 1.0 OD1 A:ASP241 2.0 19.6 1.0 O4 A:7TD502 2.1 22.9 1.0 O1 A:7TD502 2.1 22.2 1.0 NE2 A:HIS237 2.1 15.3 1.0 CG A:ASP241 2.8 19.2 1.0 C2 A:7TD502 2.8 23.1 1.0 OD2 A:ASP241 2.9 18.4 1.0 N3 A:7TD502 2.9 23.4 1.0 CE1 A:HIS78 3.0 18.9 1.0 CD2 A:HIS78 3.0 18.6 1.0 CD2 A:HIS237 3.0 15.8 1.0 CE1 A:HIS237 3.1 15.3 1.0 OG1 A:THR190 4.0 20.1 1.0 ND1 A:HIS78 4.1 20.6 1.0 CG A:HIS78 4.1 18.9 1.0 CG A:HIS237 4.2 15.9 1.0 ND1 A:HIS237 4.2 16.8 1.0 CG A:GLU77 4.2 23.6 1.0 CB A:ASP241 4.2 16.6 1.0 CB A:THR190 4.2 21.3 1.0 C1 A:7TD502 4.3 20.3 1.0 OE2 A:GLU77 4.4 22.3 1.0 CE1 A:HIS264 4.8 20.9 1.0 O A:HIS237 4.8 16.6 1.0 CD A:GLU77 4.8 34.7 1.0 C5 A:7TD502 4.9 19.4 1.0 CA A:ASP241 4.9 14.1 1.0 CA A:THR190 4.9 15.1 1.0 C3 A:7TD502 5.0 21.3 1.0 N2 A:7TD502 5.0 20.2 1.0

Zinc binding site 2 out of 2 in the Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pseudomonas Aeruginosa Lpxc in Complex with Nvs-Lpxc-01 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:19.3 occ:1.00 NE2 B:HIS78 2.0 22.1 1.0 O1 B:7TD502 2.0 24.0 1.0 OD1 B:ASP241 2.0 18.3 1.0 NE2 B:HIS237 2.1 18.4 1.0 O4 B:7TD502 2.2 24.3 1.0 CG B:ASP241 2.8 20.4 1.0 OD2 B:ASP241 2.8 17.8 1.0 C2 B:7TD502 2.8 22.0 1.0 N3 B:7TD502 3.0 22.5 1.0 CE1 B:HIS78 3.0 22.4 1.0 CD2 B:HIS78 3.0 22.2 1.0 CE1 B:HIS237 3.1 18.1 1.0 CD2 B:HIS237 3.1 18.4 1.0 OG1 B:THR190 4.0 18.9 1.0 ND1 B:HIS78 4.1 23.1 1.0 CG B:HIS78 4.1 21.0 1.0 CG B:HIS237 4.2 18.0 1.0 ND1 B:HIS237 4.2 19.2 1.0 CB B:ASP241 4.2 17.5 1.0 CB B:THR190 4.2 19.7 1.0 C1 B:7TD502 4.3 20.9 1.0 CG B:GLU77 4.3 21.8 1.0 OE2 B:GLU77 4.4 24.5 1.0 CE1 B:HIS264 4.7 23.8 1.0 C5 B:7TD502 4.8 20.8 1.0 O B:HIS237 4.8 17.1 1.0 CA B:ASP241 4.8 15.7 1.0 C3 B:7TD502 4.9 21.6 1.0 CA B:THR190 4.9 15.5 1.0 CD B:GLU77 4.9 25.5 1.0 NE2 B:HIS264 4.9 23.9 1.0 N2 B:7TD502 5.0 20.9 1.0

G.Piizzi, D.T.Parker, Y.Peng, M.Dobler, A.Patnaik, S.Wattanasin, E.Liu, F.Lenoir, J.Nunez, J.Kerrigan, D.Mckenney, C.Osborne, D.Yu, L.Lanieri, J.Bojkovic, J.Dzink-Fox, M.D.Lilly, E.R.Sprague, Y.Lu, H.Wang, S.Ranjitkar, L.Xie, B.Wang, M.Glick, L.G.Hamann, R.Tommasi, X.Yang, C.R.Dean. Design, Synthesis, and Properties of A Potent Inhibitor of Pseudomonas Aeruginosa Deacetylase Lpxc. J. Med. Chem. V. 60 5002 2017.
ISSN: ISSN 1520-4804
PubMed: 28549219
DOI: 10.1021/ACS.JMEDCHEM.7B00377