Zinc in PDB 7ci5: Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor:
3.5.1.108;

The structure of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7ci5 was solved by M.Mima, L.M.Baker, A.Surgenor, A.Robertson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.78 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.311, 50.470, 145.857, 76.73, 76.94, 60.85
R / Rfree (%)	21.1 / 28.3

The structure of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Zinc atom in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor (pdb code 7ci5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7ci5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:33.6 occ:1.00 NE2 A:HIS237 1.8 34.2 1.0 N11 A:FXX301 2.0 39.5 1.0 NE2 A:HIS78 2.0 33.7 1.0 OD1 A:ASP241 2.2 32.6 1.0 O12 A:FXX301 2.3 43.3 1.0 CE1 A:HIS237 2.7 33.2 1.0 C10 A:FXX301 2.9 42.8 1.0 CG A:ASP241 2.9 34.4 1.0 CD2 A:HIS237 2.9 33.8 1.0 CE1 A:HIS78 2.9 35.1 1.0 C9 A:FXX301 3.0 43.1 1.0 OD2 A:ASP241 3.0 37.9 1.0 CD2 A:HIS78 3.0 32.8 1.0 C17 A:FXX301 3.4 45.0 1.0 ND1 A:HIS237 3.8 31.2 1.0 CG A:HIS237 4.0 31.1 1.0 OE2 A:GLU77 4.0 36.4 1.0 ND1 A:HIS78 4.1 34.0 1.0 CG A:GLU77 4.1 34.4 1.0 CG A:HIS78 4.2 32.4 1.0 N8 A:FXX301 4.3 43.5 1.0 CB A:ASP241 4.4 32.0 1.0 CD A:GLU77 4.6 35.3 1.0 C18 A:FXX301 4.6 47.4 1.0 O A:HIS237 4.9 31.8 1.0 CD2 A:LEU240 4.9 26.6 1.0 CA A:ASP241 5.0 30.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:32.2 occ:1.00 NE2 B:HIS78 1.8 39.1 1.0 NE2 B:HIS237 1.9 36.6 1.0 N11 B:FXX301 2.0 36.9 1.0 OD1 B:ASP241 2.3 29.4 1.0 O12 B:FXX301 2.4 43.1 1.0 CE1 B:HIS78 2.8 39.8 1.0 CE1 B:HIS237 2.8 36.5 1.0 C10 B:FXX301 2.9 41.1 1.0 CD2 B:HIS78 2.9 38.2 1.0 CD2 B:HIS237 2.9 36.3 1.0 CG B:ASP241 2.9 32.6 1.0 OD2 B:ASP241 3.0 36.5 1.0 C9 B:FXX301 3.0 41.8 1.0 C17 B:FXX301 3.3 44.3 1.0 OE2 B:GLU77 3.9 38.3 1.0 ND1 B:HIS78 3.9 38.4 1.0 ND1 B:HIS237 3.9 35.0 1.0 CG B:HIS78 4.0 36.0 1.0 CG B:HIS237 4.0 34.5 1.0 CG B:GLU77 4.1 35.8 1.0 N8 B:FXX301 4.4 44.3 1.0 CB B:ASP241 4.4 31.3 1.0 CD B:GLU77 4.5 36.5 1.0 C18 B:FXX301 4.5 45.4 1.0 O B:HIS237 4.8 30.2 1.0 O B:GLY105 5.0 33.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:29.4 occ:1.00 NE2 C:HIS237 1.8 23.0 1.0 NE2 C:HIS78 1.8 27.4 1.0 N11 C:FXX301 2.1 30.1 1.0 OD1 C:ASP241 2.2 30.3 1.0 O12 C:FXX301 2.3 31.1 1.0 CE1 C:HIS237 2.6 23.8 1.0 CE1 C:HIS78 2.7 27.5 1.0 OD2 C:ASP241 2.8 29.4 1.0 CG C:ASP241 2.8 29.2 1.0 C10 C:FXX301 2.9 30.6 1.0 CD2 C:HIS78 2.9 27.2 1.0 CD2 C:HIS237 3.0 22.0 1.0 C9 C:FXX301 3.0 30.7 1.0 C17 C:FXX301 3.3 32.3 1.0 ND1 C:HIS237 3.8 23.0 1.0 ND1 C:HIS78 3.9 25.1 1.0 CG C:HIS237 4.0 22.7 1.0 CG C:HIS78 4.0 26.9 1.0 OE2 C:GLU77 4.2 34.8 1.0 CG C:GLU77 4.2 34.4 1.0 CB C:ASP241 4.3 29.4 1.0 N8 C:FXX301 4.3 31.2 1.0 C18 C:FXX301 4.5 34.9 1.0 CD C:GLU77 4.8 36.0 1.0 O C:HIS237 4.9 22.9 1.0 CD2 C:LEU240 4.9 27.4 1.0 CA C:ASP241 4.9 28.4 1.0 O C:GLY105 5.0 28.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:26.9 occ:1.00 NE2 D:HIS237 1.6 27.3 1.0 NE2 D:HIS78 1.8 28.3 1.0 OD1 D:ASP241 2.2 26.8 1.0 N11 D:FXX301 2.2 29.8 1.0 O12 D:FXX301 2.4 30.1 1.0 CE1 D:HIS237 2.4 27.1 1.0 CE1 D:HIS78 2.8 27.7 1.0 OD2 D:ASP241 2.8 29.3 1.0 CG D:ASP241 2.8 27.8 1.0 CD2 D:HIS237 2.8 26.4 1.0 CD2 D:HIS78 2.8 28.2 1.0 C10 D:FXX301 3.0 29.6 1.0 C9 D:FXX301 3.0 30.4 1.0 C17 D:FXX301 3.4 31.2 1.0 ND1 D:HIS237 3.6 26.6 1.0 CG D:HIS237 3.8 26.3 1.0 ND1 D:HIS78 3.9 26.1 1.0 CG D:HIS78 3.9 27.9 1.0 CG D:GLU77 4.1 31.8 1.0 OE2 D:GLU77 4.1 34.2 1.0 CB D:ASP241 4.3 29.0 1.0 N8 D:FXX301 4.3 29.1 1.0 C18 D:FXX301 4.6 33.5 1.0 CD D:GLU77 4.6 32.9 1.0 O D:HIS237 4.8 28.4 1.0 CA D:ASP241 4.9 28.4 1.0 O D:GLY105 5.0 31.6 1.0

Y.Yamada, H.Takashima, D.L.Walmsley, F.Ushiyama, Y.Matsuda, H.Kanazawa, T.Yamaguchi-Sasaki, N.Tanaka-Yamamoto, J.Yamagishi, R.Kurimoto-Tsuruta, Y.Ogata, N.Ohtake, H.Angove, L.Baker, R.Harris, A.Macias, A.Robertson, A.Surgenor, H.Watanabe, K.Nakano, M.Mima, K.Iwamoto, A.Okada, I.Takata, K.Hitaka, A.Tanaka, K.Fujita, H.Sugiyama, R.E.Hubbard. Fragment-Based Discovery of Novel Non-Hydroxamate Lpxc Inhibitors with Antibacterial Activity. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33210531
DOI: 10.1021/ACS.JMEDCHEM.0C01215