Zinc in PDB 4j3d: Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor

The structure of Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor, PDB code: 4j3d was solved by S.Lahiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	156.88 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.762, 156.878, 49.334, 90.00, 102.40, 90.00
R / Rfree (%)	20.1 / 28.1

The binding sites of Zinc atom in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor (pdb code 4j3d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor, PDB code: 4j3d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor


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 A Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:23.5 occ:1.00 NE2 A:HIS78 2.1 26.3 1.0 O30 A:1JS303 2.1 24.2 1.0 OD1 A:ASP241 2.2 16.1 1.0 CE1 A:HIS237 2.2 20.0 1.0 O32 A:1JS303 2.4 23.2 1.0 OD2 A:ASP241 2.7 22.3 1.0 CG A:ASP241 2.8 19.7 1.0 C29 A:1JS303 2.8 25.6 1.0 N31 A:1JS303 3.0 25.8 1.0 CD2 A:HIS78 3.0 24.6 1.0 NE2 A:HIS237 3.0 18.2 1.0 CE1 A:HIS78 3.1 30.4 1.0 ND1 A:HIS237 3.2 20.8 1.0 OE2 A:GLU77 4.0 19.1 1.0 CG A:GLU77 4.1 20.3 1.0 OG1 A:THR190 4.2 19.2 1.0 CG A:HIS78 4.2 23.0 1.0 ND1 A:HIS78 4.2 28.5 1.0 CD2 A:HIS237 4.2 16.0 1.0 C18 A:1JS303 4.2 24.8 1.0 CB A:ASP241 4.2 19.7 1.0 CG A:HIS237 4.3 20.9 1.0 CB A:THR190 4.3 22.5 1.0 C20 A:1JS303 4.5 28.0 1.0 CD A:GLU77 4.6 21.6 1.0 ZN A:ZN302 4.7 34.9 1.0 O A:HIS237 4.9 20.6 1.0 CA A:ASP241 4.9 20.4 1.0 N17 A:1JS303 4.9 22.5 1.0

Zinc binding site 2 out of 4 in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor


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 A Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:34.9 occ:1.00 N31 A:1JS303 1.9 25.8 1.0 NE2 A:HIS264 2.0 23.5 1.0 O A:MET62 2.2 29.6 1.0 O A:HOH402 2.3 19.5 1.0 O32 A:1JS303 2.7 23.2 1.0 CD2 A:HIS264 2.8 24.8 1.0 C29 A:1JS303 3.0 25.6 1.0 CE1 A:HIS264 3.1 23.0 1.0 C A:MET62 3.1 30.3 1.0 C18 A:1JS303 3.3 24.8 1.0 C20 A:1JS303 3.8 28.0 1.0 OE2 A:GLU77 3.9 19.1 1.0 N A:SER63 3.9 28.8 1.0 CG A:HIS264 4.0 23.1 1.0 CA A:MET62 4.0 32.2 1.0 CA A:SER63 4.0 28.0 1.0 O30 A:1JS303 4.1 24.2 1.0 ND1 A:HIS264 4.1 22.8 1.0 O A:HOH429 4.2 22.0 1.0 NZ A:LYS238 4.3 33.2 1.0 OD2 A:ASP241 4.3 22.3 1.0 N17 A:1JS303 4.7 22.5 1.0 ZN A:ZN301 4.7 23.5 1.0 CB A:MET62 4.8 32.3 1.0 CD A:GLU77 4.8 21.6 1.0 CG A:ASP241 4.8 19.7 1.0 O16 A:1JS303 4.8 27.9 1.0 CB A:SER63 4.9 28.6 1.0

Zinc binding site 3 out of 4 in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.4 occ:1.00 OD1 B:ASP241 2.0 21.0 1.0 O30 B:1JS303 2.1 29.1 1.0 NE2 B:HIS78 2.1 24.2 1.0 NE2 B:HIS237 2.2 25.2 1.0 O32 B:1JS303 2.4 29.9 1.0 CG B:ASP241 2.7 24.5 1.0 OD2 B:ASP241 2.7 28.5 1.0 C29 B:1JS303 2.8 32.3 1.0 N31 B:1JS303 2.9 31.3 1.0 CD2 B:HIS237 3.0 24.3 1.0 CD2 B:HIS78 3.1 24.9 1.0 CE1 B:HIS78 3.1 26.1 1.0 CE1 B:HIS237 3.2 24.3 1.0 OG1 B:THR190 4.1 25.7 1.0 C18 B:1JS303 4.2 32.3 1.0 CB B:ASP241 4.2 23.4 1.0 CG B:HIS237 4.2 25.5 1.0 OE2 B:GLU77 4.2 25.8 1.0 CG B:GLU77 4.2 23.0 1.0 ND1 B:HIS78 4.2 27.2 1.0 ND1 B:HIS237 4.2 23.4 1.0 CG B:HIS78 4.2 25.0 1.0 C20 B:1JS303 4.4 35.8 1.0 CB B:THR190 4.5 26.5 1.0 ZN B:ZN302 4.7 40.5 1.0 CD B:GLU77 4.7 22.4 1.0 CA B:ASP241 4.8 23.5 1.0 N17 B:1JS303 4.9 31.0 1.0 O B:HIS237 5.0 26.7 1.0

Zinc binding site 4 out of 4 in the Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pseudomonas Aeruginosa Lpxc in Complex with A Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:40.5 occ:1.00 N31 B:1JS303 1.9 31.3 1.0 NE2 B:HIS264 2.2 26.8 1.0 O B:MET62 2.3 38.6 1.0 O B:HOH402 2.3 18.9 1.0 O32 B:1JS303 2.8 29.9 1.0 CD2 B:HIS264 2.8 28.7 1.0 C29 B:1JS303 2.9 32.3 1.0 C B:MET62 3.2 39.0 1.0 C18 B:1JS303 3.3 32.3 1.0 CE1 B:HIS264 3.3 27.6 1.0 C20 B:1JS303 3.9 35.8 1.0 CA B:MET62 3.9 40.4 1.0 O30 B:1JS303 4.0 29.1 1.0 OE2 B:GLU77 4.0 25.8 1.0 N B:SER63 4.1 37.0 1.0 OD2 B:ASP241 4.1 28.5 1.0 CG B:HIS264 4.1 28.3 1.0 CA B:SER63 4.2 35.6 1.0 NZ B:LYS238 4.3 28.3 1.0 ND1 B:HIS264 4.3 29.5 1.0 O B:HOH439 4.3 29.3 1.0 O B:HOH447 4.6 50.4 1.0 N17 B:1JS303 4.6 31.0 1.0 O B:HOH528 4.7 36.4 1.0 ZN B:ZN301 4.7 30.4 1.0 CB B:MET62 4.7 41.0 1.0 O16 B:1JS303 4.7 35.0 1.0 CG B:ASP241 4.7 24.5 1.0 O B:THR61 4.9 42.6 1.0 CB B:SER63 5.0 35.9 1.0 CD B:GLU77 5.0 22.4 1.0

M.R.Hale, P.Hill, S.Lahiri, M.D.Miller, P.Ross, R.Alm, N.Gao, A.Kutschke, M.Johnstone, B.Prince, J.Thresher, W.Yang. Exploring the Udp Pocket of Lpxc Through Amino Acid Analogs. Bioorg.Med.Chem.Lett. V. 23 2362 2013.
ISSN: ISSN 0960-894X
PubMed: 23499237
DOI: 10.1016/J.BMCL.2013.02.055