Manganese in PDB 8qjz: Crystal Structure of E. Coli Lpxh in Complex with Lipid X

The structure of Crystal Structure of E. Coli Lpxh in Complex with Lipid X, PDB code: 8qjz 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)	30.00 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.827, 81.392, 33.127, 90, 100.32, 90
R / Rfree (%)	17.1 / 18.7

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

Manganese binding site 1 out of 2 in the Crystal Structure of E. Coli Lpxh in Complex with Lipid X


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of E. Coli Lpxh in Complex with Lipid X within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:14.4 occ:1.00 O A:HOH471 2.1 16.5 1.0 OD1 A:ASP8 2.1 12.4 1.0 NE2 A:HIS10 2.2 15.9 1.0 OD2 A:ASP41 2.2 14.3 1.0 NE2 A:HIS197 2.2 17.5 1.0 O A:HOH475 2.4 27.3 1.0 CE1 A:HIS10 3.0 18.8 1.0 CE1 A:HIS197 3.1 19.7 1.0 CG A:ASP8 3.1 11.7 1.0 CG A:ASP41 3.2 12.0 1.0 MN A:MN302 3.3 15.7 1.0 CD2 A:HIS197 3.3 15.9 1.0 CD2 A:HIS10 3.4 18.0 1.0 CB A:ASP41 3.5 10.9 1.0 O A:HOH424 3.6 27.2 1.0 CB A:ASP8 3.7 10.9 1.0 CA A:ASP8 4.1 10.1 1.0 OD2 A:ASP8 4.2 13.2 1.0 ND1 A:HIS10 4.2 19.7 1.0 O A:HIS195 4.2 14.0 1.0 ND1 A:HIS197 4.3 19.3 1.0 CG A:HIS10 4.4 15.9 1.0 OD1 A:ASP41 4.4 12.1 1.0 CG A:HIS197 4.4 16.6 1.0 CE1 A:HIS114 4.5 13.4 1.0 CA A:HIS195 4.6 13.2 1.0 NE2 A:HIS114 4.6 13.7 1.0 C A:HIS195 4.8 14.0 1.0 O A:HOH589 4.8 39.2 1.0 OD1 A:ASN79 4.8 15.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of E. Coli Lpxh in Complex with Lipid X


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of E. Coli Lpxh in Complex with Lipid X within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:15.7 occ:1.00 OD1 A:ASN79 2.0 15.2 1.0 O A:HOH471 2.1 16.5 1.0 NE2 A:HIS114 2.2 13.7 1.0 OD2 A:ASP41 2.2 14.3 1.0 ND1 A:HIS195 2.3 14.6 1.0 CE1 A:HIS114 3.1 13.4 1.0 CG A:ASP41 3.1 12.0 1.0 CE1 A:HIS195 3.2 14.6 1.0 CG A:ASN79 3.2 14.1 1.0 CD2 A:HIS114 3.3 12.3 1.0 O A:HOH424 3.3 27.2 1.0 MN A:MN301 3.3 14.4 1.0 CG A:HIS195 3.3 13.2 1.0 OD1 A:ASP41 3.6 12.1 1.0 CA A:HIS195 3.6 13.2 1.0 CB A:HIS195 3.7 12.9 1.0 OD1 A:ASP8 3.8 12.4 1.0 ND2 A:ASN79 3.8 15.6 1.0 O A:HIS195 4.0 14.0 1.0 O A:HOH475 4.1 27.3 1.0 N A:ASN79 4.2 12.1 1.0 ND1 A:HIS114 4.3 11.8 1.0 C A:HIS195 4.3 14.0 1.0 NE2 A:HIS195 4.3 14.8 1.0 CB A:ASN79 4.4 13.6 1.0 CB A:ASP41 4.4 10.9 1.0 CG A:HIS114 4.4 12.2 1.0 CD2 A:HIS195 4.4 14.2 1.0 N A:HIS195 4.5 12.2 1.0 NE2 A:HIS197 4.8 17.5 1.0 CA A:ASN79 4.9 12.9 1.0 CG A:ASP8 4.9 11.7 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