Manganese in PDB 8qka: Structure of K. Pneumoniae Lpxh in Complex with Jedi-852

The structure of Structure of K. Pneumoniae Lpxh in Complex with Jedi-852, PDB code: 8qka 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)	29.38 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.013, 60.013, 284.658, 90, 90, 120
R / Rfree (%)	21.9 / 26.4

The binding sites of Manganese atom in the Structure of K. Pneumoniae Lpxh in Complex with Jedi-852 (pdb code 8qka). 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 K. Pneumoniae Lpxh in Complex with Jedi-852, PDB code: 8qka:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of K. Pneumoniae Lpxh in Complex with Jedi-852


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of K. Pneumoniae Lpxh in Complex with Jedi-852 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:30.6 occ:1.00 OD1 A:ASP8 2.1 35.5 1.0 O A:HOH416 2.1 27.8 1.0 NE2 A:HIS10 2.2 36.3 1.0 NE2 A:HIS197 2.2 33.8 1.0 OD2 A:ASP41 2.3 27.0 1.0 CE1 A:HIS10 2.8 39.4 1.0 CG A:ASP8 3.0 28.1 1.0 CD2 A:HIS197 3.2 31.4 1.0 CE1 A:HIS197 3.2 35.8 1.0 MN A:MN302 3.3 30.8 1.0 CG A:ASP41 3.3 29.4 1.0 CD2 A:HIS10 3.4 32.9 1.0 CB A:ASP8 3.5 27.2 1.0 CB A:ASP41 3.6 28.4 1.0 O A:HOH430 3.6 37.4 1.0 O A:HIS195 3.9 34.8 1.0 CA A:ASP8 4.1 27.5 1.0 ND1 A:HIS10 4.1 36.6 1.0 OD2 A:ASP8 4.1 29.2 1.0 CA A:HIS195 4.3 27.0 1.0 ND1 A:HIS197 4.3 35.6 1.0 CG A:HIS10 4.3 33.1 1.0 CG A:HIS197 4.3 32.5 1.0 CE1 A:HIS114 4.4 28.7 1.0 C A:HIS195 4.4 31.2 1.0 OD1 A:ASP41 4.5 30.7 1.0 NE2 A:HIS114 4.6 26.4 1.0 N A:HIS195 4.8 27.8 1.0 CD1 A:ILE171 4.8 61.5 1.0 ND1 A:HIS195 4.8 29.5 1.0

Manganese binding site 2 out of 2 in the Structure of K. Pneumoniae Lpxh in Complex with Jedi-852


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of K. Pneumoniae Lpxh in Complex with Jedi-852 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:30.8 occ:1.00 OD2 A:ASP41 2.1 27.0 1.0 O A:HOH416 2.1 27.8 1.0 OD1 A:ASN79 2.2 30.2 1.0 NE2 A:HIS114 2.2 26.4 1.0 ND1 A:HIS195 2.3 29.5 1.0 CE1 A:HIS114 2.9 28.7 1.0 CG A:ASP41 3.0 29.4 1.0 CE1 A:HIS195 3.2 32.5 1.0 CG A:ASN79 3.3 34.9 1.0 MN A:MN301 3.3 30.6 1.0 CG A:HIS195 3.3 25.7 1.0 O A:HOH430 3.3 37.4 1.0 CD2 A:HIS114 3.4 28.1 1.0 OD1 A:ASP41 3.4 30.7 1.0 CA A:HIS195 3.6 27.0 1.0 CB A:HIS195 3.7 26.7 1.0 OD1 A:ASP8 3.8 35.5 1.0 ND2 A:ASN79 3.9 31.0 1.0 O A:HIS195 4.0 34.8 1.0 ND1 A:HIS114 4.2 23.0 1.0 N A:ASN79 4.2 31.6 1.0 CB A:ASP41 4.3 28.4 1.0 C A:HIS195 4.3 31.2 1.0 NE2 A:HIS195 4.4 31.6 1.0 CG A:HIS114 4.4 25.1 1.0 CD2 A:HIS195 4.4 31.4 1.0 CB A:ASN79 4.5 35.8 1.0 N A:HIS195 4.6 27.8 1.0 CA A:ASN79 4.9 32.4 1.0 CG A:ASP8 4.9 28.1 1.0 CE1 A:HIS10 5.0 39.4 1.0 NE2 A:HIS197 5.0 33.8 1.0 NE2 A:HIS10 5.0 36.3 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