Manganese in PDB 8qk9: Structure of E. Coli Lpxh in Complex with Jedi-1444

The structure of Structure of E. Coli Lpxh in Complex with Jedi-1444, PDB code: 8qk9 was solved by S.Sooriyaarachchi, T.Bergfors, T.A.Jones, S.L.Mowbray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.309, 81.178, 32.974, 90, 103.32, 90
R / Rfree (%)	17.8 / 21.2

The structure of Structure of E. Coli Lpxh in Complex with Jedi-1444 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Manganese atom in the Structure of E. Coli Lpxh in Complex with Jedi-1444 (pdb code 8qk9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of E. Coli Lpxh in Complex with Jedi-1444, PDB code: 8qk9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of E. Coli Lpxh in Complex with Jedi-1444


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of E. Coli Lpxh in Complex with Jedi-1444 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:37.9 occ:1.00 OD1 A:ASP8 2.1 30.2 1.0 O A:HOH436 2.2 32.8 1.0 NE2 A:HIS197 2.2 43.0 1.0 NE2 A:HIS10 2.3 40.0 1.0 OD2 A:ASP41 2.3 31.6 1.0 CE1 A:HIS10 3.1 42.5 1.0 CE1 A:HIS197 3.1 39.5 1.0 CG A:ASP8 3.2 32.0 1.0 CG A:ASP41 3.3 29.8 1.0 CD2 A:HIS197 3.3 39.2 1.0 CD2 A:HIS10 3.3 37.8 1.0 MN A:MN302 3.4 32.7 1.0 O A:HOH465 3.5 43.4 1.0 CB A:ASP41 3.5 27.3 1.0 CB A:ASP8 3.7 28.1 1.0 O A:HIS195 4.1 34.3 1.0 CA A:ASP8 4.1 26.9 1.0 OD2 A:ASP8 4.2 33.4 1.0 ND1 A:HIS10 4.3 43.1 1.0 ND1 A:HIS197 4.3 40.4 1.0 CA A:HIS195 4.4 28.5 1.0 CG A:HIS197 4.4 43.2 1.0 CG A:HIS10 4.4 36.2 1.0 OD1 A:ASP41 4.4 30.6 1.0 CE1 A:HIS114 4.5 24.7 1.0 C A:HIS195 4.6 30.0 1.0 NE2 A:HIS114 4.6 27.8 1.0 CD1 A:ILE171 4.8 58.1 1.0 N A:HIS195 4.8 28.6 1.0 OD1 A:ASN79 5.0 32.6 1.0

Manganese binding site 2 out of 2 in the Structure of E. Coli Lpxh in Complex with Jedi-1444


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of E. Coli Lpxh in Complex with Jedi-1444 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:32.7 occ:1.00 OD1 A:ASN79 2.1 32.6 1.0 O A:HOH436 2.1 32.8 1.0 OD2 A:ASP41 2.2 31.6 1.0 NE2 A:HIS114 2.3 27.8 1.0 ND1 A:HIS195 2.4 33.4 1.0 CG A:ASP41 3.1 29.8 1.0 CE1 A:HIS114 3.2 24.7 1.0 O A:HOH465 3.2 43.4 1.0 CG A:ASN79 3.2 33.6 1.0 CD2 A:HIS114 3.3 26.3 1.0 CE1 A:HIS195 3.4 37.9 1.0 MN A:MN301 3.4 37.9 1.0 CG A:HIS195 3.5 32.4 1.0 OD1 A:ASP41 3.5 30.6 1.0 CA A:HIS195 3.5 28.5 1.0 CB A:HIS195 3.8 31.1 1.0 ND2 A:ASN79 3.9 33.7 1.0 OD1 A:ASP8 3.9 30.2 1.0 O A:HIS195 4.0 34.3 1.0 N A:ASN79 4.2 30.5 1.0 C A:HIS195 4.3 30.0 1.0 ND1 A:HIS114 4.3 26.6 1.0 CB A:ASP41 4.4 27.3 1.0 CB A:ASN79 4.4 34.2 1.0 CG A:HIS114 4.4 24.9 1.0 NE2 A:HIS195 4.5 31.4 1.0 N A:HIS195 4.5 28.6 1.0 CD2 A:HIS195 4.5 35.8 1.0 CA A:ASN79 4.9 33.2 1.0

D.L.Huseby, S.Cao, E.Zamaratski, S.Sooriyaarachchi, S.Ahmad, T.Bergfors, L.Krasnova, J.Pelss, M.Ikaunieks, E.Loza, M.Katkevics, O.Bobileva, H.Cirule, B.Gukalova, S.Grinberga, M.Backlund, I.Simoff, A.T.Leber, T.Berruga-Fernandez, D.Antonov, V.R.Konda, S.Lindstrom, G.Olanders, P.Brandt, P.Baranczewski, C.Vingsbo Lundberg, E.Liepinsh, E.Suna, T.A.Jones, S.L.Mowbray, D.Hughes, A.Karlen. Antibiotic Class with Potent in Vivo Activity Targeting Lipopolysaccharide Synthesis in Gram-Negative Bacteria. Proc.Natl.Acad.Sci.Usa V. 121 74121 2024.
ISSN: ESSN 1091-6490
PubMed: 38579010
DOI: 10.1073/PNAS.2317274121