Zinc in PDB 7dem: 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: 7dem was solved by M.Mima, F.Ushiyama, Y.Matsuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.54 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.854, 66.306, 63.542, 90, 90.63, 90
R / Rfree (%)	19.4 / 23.8

The binding sites of Zinc atom in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor (pdb code 7dem). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7dem:

Zinc binding site 1 out of 1 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:Zn301 b:14.3 occ:1.00 OD1 A:ASP241 2.1 10.7 1.0 NE2 A:HIS237 2.1 9.9 1.0 N2 A:H4O302 2.1 10.5 1.0 NE2 A:HIS78 2.2 9.6 1.0 O26 A:H4O302 2.3 11.1 1.0 CG A:ASP241 2.7 11.6 1.0 OD2 A:ASP241 2.8 12.6 1.0 C1 A:H4O302 2.9 13.7 1.0 CD2 A:HIS237 3.0 9.9 1.0 CD2 A:HIS78 3.1 9.9 1.0 C24 A:H4O302 3.2 11.4 1.0 CE1 A:HIS237 3.2 9.7 1.0 C3 A:H4O302 3.2 14.2 1.0 CE1 A:HIS78 3.2 10.7 1.0 C25 A:H4O302 4.0 11.4 1.0 OG1 A:THR190 4.1 13.8 1.0 N5 A:H4O302 4.2 15.2 1.0 CB A:ASP241 4.2 11.2 1.0 CG A:HIS237 4.2 9.8 1.0 ND1 A:HIS237 4.2 10.1 1.0 C4 A:H4O302 4.3 14.3 1.0 ND1 A:HIS78 4.3 10.4 1.0 CG A:HIS78 4.3 9.4 1.0 OE2 A:GLU77 4.4 11.6 1.0 O A:HOH542 4.4 30.9 1.0 CG A:GLU77 4.4 12.0 1.0 CA A:ASP241 4.8 11.2 1.0 CE1 A:HIS264 4.9 20.6 1.0 CD A:GLU77 4.9 12.1 1.0 CA A:THR190 5.0 12.9 1.0 O A:HIS237 5.0 13.6 1.0 CB A:THR190 5.0 12.7 1.0

F.Ushiyama, H.Takashima, Y.Matsuda, Y.Ogata, N.Sasamoto, R.Kurimoto-Tsuruta, K.Ueki, N.Tanaka-Yamamoto, M.Endo, M.Mima, K.Fujita, I.Takata, S.Tsuji, H.Yamashita, H.Okumura, K.Otake, H.Sugiyama. Lead Optimization of 2-Hydroxymethyl Imidazoles As Non-Hydroxamate Lpxc Inhibitors: Discovery of TP0586532. Bioorg.Med.Chem. V. 30 15964 2020.
ISSN: ESSN 1464-3391
PubMed: 33385955
DOI: 10.1016/J.BMC.2020.115964