Zinc in PDB 3p3e: Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex

The structure of Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex, PDB code: 3p3e was solved by C.-J.Lee, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.99 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.637, 73.608, 88.308, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 19.3

The structure of Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex (pdb code 3p3e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex, PDB code: 3p3e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex


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 the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:9.5 occ:1.00 OD1 A:ASP241 2.0 10.8 1.0 O04 A:3P3501 2.1 10.8 0.6 NE2 A:HIS237 2.1 8.3 1.0 NE2 A:HIS78 2.1 8.6 1.0 O01 A:3P3501 2.1 10.7 0.6 O01 A:3P3501 2.1 11.5 0.4 O04 A:3P3501 2.4 11.0 0.4 OD2 A:ASP241 2.4 11.9 1.0 CG A:ASP241 2.6 11.4 1.0 C02 A:3P3501 2.8 12.5 0.6 N03 A:3P3501 2.8 13.8 0.6 C02 A:3P3501 2.9 13.0 0.4 CE1 A:HIS237 3.0 9.2 1.0 N03 A:3P3501 3.0 11.6 0.4 CD2 A:HIS78 3.0 10.0 1.0 CD2 A:HIS237 3.1 8.6 1.0 CE1 A:HIS78 3.1 9.8 1.0 HE1 A:HIS237 3.2 11.1 1.0 HD2 A:HIS78 3.2 12.0 1.0 HE1 A:HIS78 3.3 11.8 1.0 HD2 A:HIS237 3.3 10.3 1.0 HG3 A:GLU77 3.5 13.1 1.0 HE2 A:HIS264 3.6 17.1 1.0 HG1 A:THR190 3.6 15.1 1.0 HB A:THR190 3.8 13.3 1.0 CB A:ASP241 4.1 9.7 1.0 ND1 A:HIS237 4.1 9.2 1.0 HG2 A:GLU77 4.1 13.1 1.0 OG1 A:THR190 4.2 12.6 1.0 ND1 A:HIS78 4.2 9.9 1.0 CG A:HIS237 4.2 8.6 1.0 O A:HOH1367 4.2 31.8 1.0 CG A:HIS78 4.2 9.7 1.0 CG A:GLU77 4.2 10.9 1.0 C05 A:3P3501 4.2 14.4 0.4 C05 A:3P3501 4.3 13.5 0.6 HD23 A:LEU240 4.3 11.7 1.0 OE2 A:GLU77 4.3 12.7 1.0 NE2 A:HIS264 4.4 14.3 1.0 HA A:THR190 4.4 12.6 1.0 HA A:ASP241 4.4 10.6 1.0 CB A:THR190 4.4 11.1 1.0 HB3 A:ASP241 4.5 11.6 1.0 HB2 A:ASP241 4.5 11.6 1.0 HE1 A:HIS264 4.7 18.7 1.0 C25 A:3P3501 4.7 13.3 0.4 CA A:ASP241 4.8 8.8 1.0 CD A:GLU77 4.8 11.2 1.0 C26 A:3P3501 4.8 13.3 0.6 HD1 A:HIS237 4.9 11.0 1.0 O27 A:3P3501 4.9 20.4 0.6 O A:HIS237 4.9 8.6 1.0 N06 A:3P3501 4.9 13.5 0.6 CA A:THR190 4.9 10.5 1.0 CE1 A:HIS264 4.9 15.6 1.0 C25 A:3P3501 4.9 15.4 0.6 HD1 A:HIS78 5.0 11.9 1.0 N06 A:3P3501 5.0 13.9 0.4

Zinc binding site 2 out of 2 in the Crystal Structure of the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex


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 the Pseudomonas Aeruginosa Lpxc/Lpc-009 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:18.9 occ:1.00 ND1 A:HIS162 2.0 19.7 1.0 OE1 A:GLU219 2.1 25.6 1.0 OE2 A:GLU219 2.1 30.9 1.0 CD A:GLU219 2.4 21.2 1.0 CE1 A:HIS162 2.9 20.2 1.0 HE1 A:HIS162 3.0 24.2 1.0 HA A:HIS162 3.0 17.4 1.0 CG A:HIS162 3.1 18.3 1.0 HB3 A:HIS162 3.4 18.1 1.0 CB A:HIS162 3.6 15.1 1.0 CA A:HIS162 3.7 14.5 1.0 CG A:GLU219 3.9 21.2 1.0 HD3 A:PRO163 3.9 17.3 1.0 NE2 A:HIS162 4.1 22.8 1.0 HD2 A:PRO163 4.1 17.3 1.0 CD2 A:HIS162 4.2 21.0 1.0 HG3 A:GLU219 4.2 25.4 1.0 N A:HIS162 4.3 13.4 1.0 HG2 A:GLU219 4.3 25.4 1.0 H A:HIS162 4.4 16.1 1.0 CD A:PRO163 4.4 14.4 1.0 O A:HOH1252 4.5 31.0 1.0 HB2 A:HIS162 4.5 18.1 1.0 HB3 A:GLU219 4.5 25.1 1.0 HA A:GLU219 4.7 19.3 1.0 CB A:GLU219 4.8 20.9 1.0 HE2 A:HIS162 4.8 27.4 1.0 C A:ASP161 5.0 14.3 1.0 C A:HIS162 5.0 14.7 1.0

C.J.Lee, X.Liang, X.Chen, D.Zeng, S.H.Joo, H.S.Chung, A.W.Barb, S.M.Swanson, R.A.Nicholas, Y.Li, E.J.Toone, C.R.Raetz, P.Zhou. Species-Specific and Inhibitor-Dependent Conformations of Lpxc: Implications For Antibiotic Design. Chem.Biol. V. 18 38 2011.
ISSN: ISSN 1074-5521
PubMed: 21167751
DOI: 10.1016/J.CHEMBIOL.2010.11.011