Zinc in PDB 7k9a: Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor

All present enzymatic activity of Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor:
3.5.1.108;

The structure of Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor, PDB code: 7k9a was solved by M.Sacco, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.89 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.621, 157.351, 48.846, 90.00, 101.64, 90.00
R / Rfree (%)	16.6 / 22.2

The binding sites of Zinc atom in the Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor (pdb code 7k9a). 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 P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor, PDB code: 7k9a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide 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 with N-Hydroxyformamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:21.6 occ:1.00 O31 A:W4P401 2.0 24.9 1.0 OD1 A:ASP241 2.0 18.4 1.0 NE2 A:HIS78 2.1 20.6 1.0 NE2 A:HIS237 2.1 19.6 1.0 O33 A:W4P401 2.1 26.0 1.0 CG A:ASP241 2.7 19.4 1.0 OD2 A:ASP241 2.7 20.4 1.0 N30 A:W4P401 2.8 24.7 1.0 C32 A:W4P401 2.9 26.2 1.0 CE1 A:HIS237 2.9 18.7 1.0 CD2 A:HIS78 3.0 21.3 1.0 CE1 A:HIS78 3.1 23.8 1.0 CD2 A:HIS237 3.2 19.0 1.0 O A:HOH546 3.7 30.5 1.0 ND1 A:HIS237 4.0 19.1 1.0 OG1 A:THR190 4.1 19.2 1.0 CB A:ASP241 4.1 19.2 1.0 ND1 A:HIS78 4.2 22.7 1.0 CG A:HIS237 4.2 19.5 1.0 CG A:HIS78 4.2 21.9 1.0 C03 A:W4P401 4.2 25.1 1.0 CG A:GLU77 4.3 22.8 1.0 CB A:THR190 4.4 20.6 1.0 OE2 A:GLU77 4.5 26.2 1.0 NE2 A:HIS264 4.5 27.5 1.0 O A:HIS237 4.7 17.9 1.0 CA A:ASP241 4.8 19.1 1.0 S02 A:W4P401 4.9 28.3 1.0 CD A:GLU77 4.9 24.1 1.0 CD2 A:LEU240 5.0 22.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide 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 with N-Hydroxyformamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn406 b:25.8 occ:1.00 OD1 C:ASP241 2.0 24.8 1.0 NE2 C:HIS78 2.0 24.7 1.0 NE2 C:HIS237 2.0 22.4 1.0 O33 C:W4P402 2.1 29.1 1.0 O31 C:W4P402 2.2 32.0 1.0 CG C:ASP241 2.7 24.2 1.0 OD2 C:ASP241 2.7 25.8 1.0 C32 C:W4P402 2.9 28.7 1.0 CE1 C:HIS237 2.9 24.3 1.0 N30 C:W4P402 3.0 29.7 1.0 CE1 C:HIS78 3.0 25.9 1.0 CD2 C:HIS78 3.0 23.9 1.0 CD2 C:HIS237 3.0 23.9 1.0 O C:HOH592 4.0 38.0 1.0 ND1 C:HIS237 4.1 23.2 1.0 ND1 C:HIS78 4.1 24.4 1.0 CG C:HIS237 4.1 23.5 1.0 CB C:ASP241 4.1 23.4 1.0 CG C:HIS78 4.1 23.4 1.0 OG1 C:THR190 4.2 29.1 1.0 CG C:GLU77 4.4 29.0 1.0 CB C:THR190 4.4 28.7 1.0 C03 C:W4P402 4.4 30.5 1.0 NE2 C:HIS264 4.5 27.6 1.0 O C:HIS237 4.7 24.1 1.0 OE2 C:GLU77 4.7 32.2 1.0 CA C:ASP241 4.8 22.5 1.0 S02 C:W4P402 4.9 33.8 1.0

T.Furuya, A.B.Shapiro, J.Comita-Prevoir, E.J.Kuenstner, J.Zhang, S.D.Ribe, A.Chen, D.Hines, S.H.Moussa, N.M.Carter, M.A.Sylvester, J.A.C.Romero, C.V.Vega, M.D.Sacco, Y.Chen, J.P.O'donnell, T.F.Durand-Reville, A.A.Miller, R.A.Tommasi. N-Hydroxyformamide Lpxc Inhibitors, Their in Vivo Efficacy in A Mouse Escherichia Coli Infection Model, and Their Safety in A Rat Hemodynamic Assay. Bioorg.Med.Chem. V. 28 15826 2020.
ISSN: ESSN 1464-3391
PubMed: 33160146
DOI: 10.1016/J.BMC.2020.115826