Zinc in PDB 3fid: Lpxr From Salmonella Typhimurium

The structure of Lpxr From Salmonella Typhimurium, PDB code: 3fid was solved by L.Rutten, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.74 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.930, 127.650, 60.660, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23

The binding sites of Zinc atom in the Lpxr From Salmonella Typhimurium (pdb code 3fid). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Lpxr From Salmonella Typhimurium, PDB code: 3fid:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn297 b:35.7 occ:1.00 OD1 A:ASP44 2.1 32.1 1.0 OG A:SER1 2.1 23.5 1.0 N A:SER1 2.3 23.1 1.0 CB A:SER1 2.7 22.4 1.0 CA A:SER1 3.0 22.4 1.0 CG A:ASP44 3.0 29.4 1.0 O A:HOH475 3.1 43.2 1.0 OD2 A:ASP44 3.4 36.4 1.0 ZN A:ZN298 3.5 31.7 1.0 OXT A:PHE296 3.6 24.8 1.0 O A:HOH372 3.8 34.8 1.0 O B:HOH431 4.0 21.7 1.0 N A:ASP44 4.2 20.2 1.0 C A:SER1 4.3 22.6 1.0 CB A:ASP44 4.3 23.7 1.0 C A:PHE296 4.5 24.6 1.0 ND1 A:HIS43 4.5 21.5 1.0 O A:HOH481 4.5 39.9 1.0 O A:PHE296 4.6 25.4 1.0 O A:SER1 4.6 22.1 1.0 CE1 A:HIS43 4.8 21.0 1.0 CA A:ASP44 4.8 22.8 1.0

Zinc binding site 2 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn298 b:31.7 occ:1.00 OG A:SER1 1.9 23.5 1.0 ND1 A:HIS43 2.1 21.5 1.0 OH A:TYR41 2.3 19.0 1.0 O B:HOH431 2.4 21.7 1.0 CB A:SER1 2.9 22.4 1.0 CE1 A:HIS43 2.9 21.0 1.0 CG A:HIS43 3.2 19.0 1.0 CZ A:TYR41 3.4 16.6 1.0 ZN A:ZN297 3.5 35.7 1.0 CB A:HIS43 3.6 18.8 1.0 CA A:HIS43 3.7 18.5 1.0 OH B:TYR41 3.9 19.0 1.0 CE2 B:PHE296 4.0 24.5 1.0 OD1 A:ASP44 4.0 32.1 1.0 ZN B:ZN298 4.1 32.2 1.0 NE2 A:HIS43 4.1 21.1 1.0 CA A:SER1 4.2 22.4 1.0 CE2 A:TYR41 4.2 17.5 1.0 CE1 A:TYR41 4.2 17.9 1.0 O A:SER42 4.3 19.1 1.0 CD2 A:HIS43 4.3 22.7 1.0 N A:ASP44 4.4 20.2 1.0 C A:HIS43 4.6 18.5 1.0 N A:SER1 4.8 23.1 1.0 CD2 B:PHE296 4.8 23.3 1.0 N A:HIS43 4.8 19.0 1.0 CZ B:PHE296 4.9 23.9 1.0 C A:SER42 4.9 18.4 1.0 CE2 A:PHE296 5.0 24.3 1.0

Zinc binding site 3 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn299 b:15.4 occ:1.00 OD1 A:ASP104 1.8 17.0 1.0 NE2 A:HIS54 2.1 8.6 1.0 ND1 A:HIS84 2.1 9.8 1.0 O A:HOH338 2.3 12.8 1.0 CG A:ASP104 2.8 18.3 1.0 CE1 A:HIS54 2.9 12.6 1.0 CE1 A:HIS84 2.9 8.0 1.0 CD2 A:HIS54 3.2 11.8 1.0 OD2 A:ASP104 3.2 18.5 1.0 CG A:HIS84 3.2 9.6 1.0 CB A:HIS84 3.7 10.4 1.0 O A:HOH482 3.8 27.5 1.0 ND1 A:HIS54 4.1 13.0 1.0 NE2 A:HIS84 4.1 8.4 1.0 CB A:ASP104 4.1 16.6 1.0 NZ A:LYS146 4.2 27.1 1.0 CG A:HIS54 4.2 11.3 1.0 CD2 A:HIS84 4.3 9.2 1.0 C A:HIS84 4.5 10.9 1.0 N A:THR85 4.6 11.3 1.0 O A:HIS84 4.7 10.7 1.0 CA A:HIS84 4.7 10.7 1.0 C A:THR85 4.7 11.7 1.0 O A:HOH430 4.8 28.4 1.0 CA A:THR85 4.9 11.4 1.0 N A:GLY86 4.9 12.7 1.0 O A:THR85 5.0 11.8 1.0

Zinc binding site 4 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:13.3 occ:1.00 OD2 A:ASP29 1.9 10.7 1.0 ND1 A:HIS25 2.1 10.5 1.0 CG A:ASP29 2.7 11.9 1.0 OD1 A:ASP29 2.9 12.1 1.0 CE1 A:HIS25 2.9 16.6 1.0 CG A:HIS25 3.2 13.6 1.0 O A:HIS25 3.6 12.5 1.0 CB A:HIS25 3.7 11.6 1.0 C A:HIS25 3.7 10.9 1.0 N A:PRO26 4.0 10.4 1.0 NE2 A:HIS25 4.1 16.0 1.0 CB A:ASP29 4.2 13.8 1.0 CD2 A:HIS25 4.3 13.3 1.0 CA A:PRO26 4.3 9.9 1.0 CA A:HIS25 4.4 11.9 1.0 CD A:PRO26 4.7 10.1 1.0

Zinc binding site 5 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:27.1 occ:0.50 OG1 A:THR34 1.7 15.6 1.0 O2 A:GOL303 1.8 38.0 1.0 O A:THR34 2.3 13.0 1.0 OD2 A:ASP10 2.3 19.4 1.0 O1 A:GOL303 2.5 35.5 1.0 C2 A:GOL303 2.7 39.1 1.0 CB A:THR34 2.8 12.7 1.0 C A:THR34 2.9 12.3 1.0 CA A:THR34 3.0 12.3 1.0 C1 A:GOL303 3.0 36.9 1.0 CG A:ASP10 3.4 17.7 1.0 O A:HOH417 3.6 19.5 1.0 OD1 A:ASN9 3.7 14.3 1.0 CG2 A:THR34 3.8 13.1 1.0 OD1 A:ASP10 3.9 25.4 1.0 O A:HOH376 4.0 29.9 1.0 C3 A:GOL303 4.1 40.5 1.0 N A:ALA35 4.1 10.1 1.0 N A:THR34 4.4 11.6 1.0 N A:ASP10 4.5 12.9 1.0 CB A:ASP10 4.6 13.0 1.0 O A:HOH326 4.7 23.8 1.0 CG A:ASN9 4.7 14.0 1.0 CA A:ALA35 4.8 10.8 1.0 O A:TYR33 4.9 12.3 1.0 O3 A:GOL303 4.9 43.0 1.0 CB A:ALA35 4.9 11.1 1.0 O A:HOH457 5.0 29.9 1.0

Zinc binding site 6 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn297 b:34.2 occ:1.00 OD1 B:ASP44 2.1 30.1 1.0 N B:SER1 2.2 21.9 1.0 OG B:SER1 2.2 23.4 1.0 CB B:SER1 2.7 20.7 1.0 CA B:SER1 2.9 21.1 1.0 CG B:ASP44 3.0 27.4 1.0 O B:HOH473 3.2 39.7 1.0 ZN B:ZN298 3.4 32.2 1.0 OD2 B:ASP44 3.4 33.1 1.0 O B:HOH462 3.6 48.1 1.0 OXT B:PHE296 3.7 25.2 1.0 O B:HOH431 4.0 21.7 1.0 N B:ASP44 4.1 21.6 1.0 C B:SER1 4.2 20.8 1.0 CB B:ASP44 4.2 23.6 1.0 ND1 B:HIS43 4.3 23.6 1.0 O B:SER1 4.6 20.5 1.0 C B:PHE296 4.6 24.5 1.0 CE1 B:HIS43 4.6 24.4 1.0 O B:PHE296 4.7 25.1 1.0 O B:HOH349 4.7 42.5 1.0 CA B:ASP44 4.7 23.0 1.0 O B:ASP44 4.9 22.7 1.0

Zinc binding site 7 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn298 b:32.2 occ:1.00 OG B:SER1 1.8 23.4 1.0 ND1 B:HIS43 1.9 23.6 1.0 OH B:TYR41 2.3 19.0 1.0 O B:HOH431 2.3 21.7 1.0 CE1 B:HIS43 2.8 24.4 1.0 CB B:SER1 2.8 20.7 1.0 CG B:HIS43 3.1 21.8 1.0 CZ B:TYR41 3.4 16.3 1.0 ZN B:ZN297 3.4 34.2 1.0 CB B:HIS43 3.5 20.8 1.0 CA B:HIS43 3.7 20.4 1.0 OH A:TYR41 3.9 19.0 1.0 NE2 B:HIS43 4.0 22.9 1.0 OD1 B:ASP44 4.1 30.1 1.0 ZN A:ZN298 4.1 31.7 1.0 CD2 B:HIS43 4.1 24.0 1.0 CE1 B:TYR41 4.1 18.1 1.0 CA B:SER1 4.1 21.1 1.0 CE2 A:PHE296 4.1 24.3 1.0 CE2 B:TYR41 4.2 17.6 1.0 O B:SER42 4.3 21.0 1.0 N B:ASP44 4.4 21.6 1.0 C B:HIS43 4.6 20.8 1.0 N B:SER1 4.7 21.9 1.0 N B:HIS43 4.8 20.4 1.0 CD2 A:PHE296 4.8 24.5 1.0 CE2 B:PHE296 4.9 24.5 1.0 C B:SER42 4.9 19.6 1.0

Zinc binding site 8 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn299 b:13.2 occ:1.00 OD1 B:ASP104 1.7 13.9 1.0 NE2 B:HIS54 2.1 10.7 1.0 ND1 B:HIS84 2.1 11.6 1.0 O B:HOH327 2.1 13.0 1.0 CG B:ASP104 2.8 16.3 1.0 CE1 B:HIS84 3.0 12.9 1.0 CE1 B:HIS54 3.0 12.5 1.0 CD2 B:HIS54 3.1 11.1 1.0 CG B:HIS84 3.2 12.7 1.0 OD2 B:ASP104 3.3 18.2 1.0 CB B:HIS84 3.6 11.3 1.0 O B:HOH504 3.8 32.0 1.0 CB B:ASP104 4.1 17.0 1.0 NZ B:LYS146 4.1 27.6 1.0 ND1 B:HIS54 4.1 12.9 1.0 NE2 B:HIS84 4.2 10.0 1.0 CG B:HIS54 4.2 11.3 1.0 CD2 B:HIS84 4.3 13.2 1.0 C B:HIS84 4.5 10.9 1.0 O B:HOH433 4.6 34.6 1.0 N B:THR85 4.6 11.2 1.0 O B:HIS84 4.7 11.0 1.0 CA B:HIS84 4.7 11.0 1.0 C B:THR85 4.8 12.9 1.0 O B:HOH403 4.8 21.6 1.0 CA B:THR85 4.9 12.0 1.0 N B:GLY86 5.0 14.2 1.0 O B:THR85 5.0 13.0 1.0

Zinc binding site 9 out of 9 in the Lpxr From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Lpxr From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:22.1 occ:0.50 OG1 B:THR34 1.8 13.6 1.0 O2 B:GOL302 1.9 31.6 1.0 O B:THR34 2.2 11.7 1.0 OD2 B:ASP10 2.2 18.3 1.0 O1 B:GOL302 2.5 22.2 1.0 C2 B:GOL302 2.7 31.0 1.0 C B:THR34 2.8 11.2 1.0 CB B:THR34 2.9 11.2 1.0 CA B:THR34 2.9 11.0 1.0 C1 B:GOL302 3.1 27.6 1.0 CG B:ASP10 3.3 17.2 1.0 OD1 B:ASN9 3.6 15.2 1.0 O B:HOH375 3.6 19.2 1.0 CG2 B:THR34 3.7 12.3 1.0 OD1 B:ASP10 3.8 24.1 1.0 O B:HOH553 3.9 32.7 1.0 N B:ALA35 4.1 10.0 1.0 C3 B:GOL302 4.1 32.9 1.0 N B:THR34 4.4 10.5 1.0 N B:ASP10 4.4 13.0 1.0 CB B:ASP10 4.5 14.4 1.0 O3 B:GOL302 4.6 35.1 1.0 CG B:ASN9 4.6 13.2 1.0 O B:HOH479 4.8 30.8 1.0 CA B:ALA35 4.8 10.4 1.0 O B:TYR33 4.8 10.7 1.0 O B:HOH322 4.9 14.4 1.0 CB B:ALA35 4.9 10.2 1.0

L.Rutten, J.-P.B.A.Mannie, C.M.Stead, C.R.H.Raetz, C.M.Reynolds, A.M.J.J.Bonvin, J.P.Tommassen, M.R.Egmond, M.S.Trent, P.Gros. Active-Site Architecture and Catalytic Mechanism of the Lipid A Deacylase Lpxr of Salmonella Typhimurium Proc.Natl.Acad.Sci.Usa V. 106 1960 2009.
ISSN: ISSN 0027-8424
PubMed: 19174515
DOI: 10.1073/PNAS.0813064106