Magnesium in PDB 7ci4: 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: 7ci4 was solved by M.Mima, L.M.Baker, A.Surgenor, A.Robertson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.32 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.367, 51.180, 96.763, 90.00, 108.22, 90.00
R / Rfree (%)	18.7 / 24.1

The structure of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor (pdb code 7ci4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor, PDB code: 7ci4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1302 b:27.3 occ:1.00 O A:HOH1414 1.9 26.5 1.0 O B:HOH1440 2.0 26.4 1.0 OD1 A:ASP279 2.0 27.9 1.0 OD1 A:ASP277 2.1 25.3 1.0 O A:HOH1432 2.1 22.7 1.0 O A:HOH1530 2.1 25.2 1.0 CG A:ASP277 3.0 24.8 1.0 CG A:ASP279 3.0 31.9 1.0 OD2 A:ASP277 3.3 25.3 1.0 OD2 A:ASP279 3.4 33.7 1.0 O B:GLU138 4.1 32.2 1.0 NE2 B:GLN269 4.2 18.6 1.0 O B:HOH1438 4.3 35.6 1.0 O B:HOH1536 4.3 36.3 1.0 CB A:ASP277 4.3 21.7 1.0 CB A:ASP279 4.3 32.7 1.0 OE1 B:GLN269 4.4 21.6 1.0 O B:HOH1484 4.4 31.1 1.0 N A:ASP279 4.5 27.1 1.0 O B:HOH1500 4.6 35.6 1.0 CD A:ARG133 4.6 32.8 1.0 N A:ALA280 4.7 25.5 1.0 CA A:ASP277 4.7 23.5 1.0 CD B:GLN269 4.7 21.1 1.0 CB B:GLU139 4.8 34.2 1.0 CA A:ASP279 4.8 28.8 1.0 C A:ASP277 4.8 23.9 1.0 CG B:GLU139 4.8 41.3 1.0 OE2 B:GLU139 4.8 58.5 1.0 C A:ASP279 4.8 27.8 1.0 CB A:ALA280 4.9 24.6 1.0 NE A:ARG133 5.0 39.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of P.Aeruginosa Lpxc in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1302 b:27.2 occ:1.00 O A:HOH1446 2.0 19.3 1.0 O B:HOH1410 2.0 23.7 1.0 OD1 B:ASP279 2.0 22.4 1.0 O B:HOH1425 2.1 22.2 1.0 OD1 B:ASP277 2.1 24.9 1.0 O A:HOH1509 2.1 20.3 1.0 CG B:ASP279 3.0 24.2 1.0 CG B:ASP277 3.1 22.6 1.0 OD2 B:ASP279 3.3 24.8 1.0 OD2 B:ASP277 3.4 23.1 1.0 O A:HOH1423 4.1 26.9 1.0 O A:GLU138 4.1 21.7 1.0 NE2 A:GLN269 4.1 24.2 1.0 O B:HOH1507 4.2 33.9 1.0 O B:HOH1465 4.2 23.6 1.0 CB B:ASP279 4.3 24.3 1.0 OE1 A:GLN269 4.3 19.6 1.0 NE B:ARG133 4.4 26.7 1.0 CB B:ASP277 4.4 22.3 1.0 O A:HOH1440 4.5 23.9 1.0 CD B:ARG133 4.6 25.4 1.0 CG A:GLU139 4.6 29.9 1.0 CB A:GLU139 4.7 26.7 1.0 CD A:GLN269 4.7 21.3 1.0 N B:ASP279 4.7 24.5 1.0 CA B:ASP277 4.8 22.8 1.0 N B:ALA280 4.8 22.8 1.0 CA B:ASP279 4.8 24.7 1.0 C B:ASP277 4.8 22.8 1.0 CA A:GLU139 4.9 25.8 1.0 C B:ASP279 4.9 22.5 1.0

Y.Yamada, H.Takashima, D.L.Walmsley, F.Ushiyama, Y.Matsuda, H.Kanazawa, T.Yamaguchi-Sasaki, N.Tanaka-Yamamoto, J.Yamagishi, R.Kurimoto-Tsuruta, Y.Ogata, N.Ohtake, H.Angove, L.Baker, R.Harris, A.Macias, A.Robertson, A.Surgenor, H.Watanabe, K.Nakano, M.Mima, K.Iwamoto, A.Okada, I.Takata, K.Hitaka, A.Tanaka, K.Fujita, H.Sugiyama, R.E.Hubbard. Fragment-Based Discovery of Novel Non-Hydroxamate Lpxc Inhibitors with Antibacterial Activity. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33210531
DOI: 10.1021/ACS.JMEDCHEM.0C01215