Manganese in PDB 8qk5: Structure of K. Pneumoniae Lpxh in Complex with Ebl-3647

The structure of Structure of K. Pneumoniae Lpxh in Complex with Ebl-3647, PDB code: 8qk5 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)	29.65 / 1.95
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.418, 60.418, 287.692, 90, 90, 120
R / Rfree (%)	24 / 28.2

The binding sites of Manganese atom in the Structure of K. Pneumoniae Lpxh in Complex with Ebl-3647 (pdb code 8qk5). 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 Ebl-3647, PDB code: 8qk5:
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 Ebl-3647


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 Ebl-3647 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:44.0 occ:1.00 OD1 A:ASP8 2.1 41.2 1.0 O A:HOH428 2.1 41.7 1.0 OD2 A:ASP41 2.2 37.5 1.0 NE2 A:HIS197 2.2 43.8 1.0 NE2 A:HIS10 2.2 44.4 1.0 CE1 A:HIS10 2.7 47.9 1.0 CE1 A:HIS197 3.0 43.8 1.0 MN A:MN302 3.0 58.3 1.0 CG A:ASP8 3.2 41.4 1.0 CG A:ASP41 3.2 40.9 1.0 CD2 A:HIS197 3.4 39.5 1.0 CB A:ASP41 3.5 37.4 1.0 CD2 A:HIS10 3.5 45.2 1.0 CB A:ASP8 3.7 34.5 1.0 ND1 A:HIS10 4.0 47.9 1.0 O A:HIS195 4.1 41.5 1.0 CA A:ASP8 4.1 38.2 1.0 OD2 A:ASP8 4.2 38.6 1.0 ND1 A:HIS197 4.2 44.3 1.0 OD1 A:ASP41 4.4 47.1 1.0 CG A:HIS10 4.4 42.4 1.0 CG A:HIS197 4.4 44.5 1.0 CA A:HIS195 4.5 36.1 1.0 CE1 A:HIS114 4.6 38.6 1.0 OD1 A:ASN79 4.6 45.9 1.0 NE2 A:HIS114 4.6 39.2 1.0 CD1 A:ILE171 4.7 57.6 1.0 C A:HIS195 4.7 36.2 1.0 ND1 A:HIS195 4.9 40.1 1.0 CG A:ARG80 5.0 37.1 1.0 N A:HIS195 5.0 38.1 1.0

Manganese binding site 2 out of 2 in the Structure of K. Pneumoniae Lpxh in Complex with Ebl-3647


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 Ebl-3647 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:58.3 occ:1.00 OD1 A:ASN79 2.1 45.9 1.0 OD2 A:ASP41 2.2 37.5 1.0 O A:HOH428 2.2 41.7 1.0 NE2 A:HIS114 2.3 39.2 1.0 ND1 A:HIS195 2.3 40.1 1.0 MN A:MN301 3.0 44.0 1.0 CE1 A:HIS114 3.1 38.6 1.0 CG A:ASP41 3.1 40.9 1.0 CE1 A:HIS195 3.2 37.3 1.0 CG A:ASN79 3.3 42.5 1.0 CG A:HIS195 3.4 38.9 1.0 CD2 A:HIS114 3.4 39.8 1.0 CA A:HIS195 3.5 36.1 1.0 OD1 A:ASP8 3.6 41.2 1.0 OD1 A:ASP41 3.6 47.1 1.0 CB A:HIS195 3.8 37.6 1.0 O A:HIS195 3.9 41.5 1.0 ND2 A:ASN79 4.1 43.8 1.0 C A:HIS195 4.2 36.2 1.0 N A:ASN79 4.2 39.6 1.0 CB A:ASP41 4.3 37.4 1.0 ND1 A:HIS114 4.3 35.0 1.0 NE2 A:HIS195 4.3 36.5 1.0 CB A:ASN79 4.4 42.1 1.0 CD2 A:HIS195 4.5 38.5 1.0 N A:HIS195 4.5 38.1 1.0 CG A:HIS114 4.5 33.8 1.0 NE2 A:HIS197 4.6 43.8 1.0 CG A:ASP8 4.7 41.4 1.0 CA A:ASN79 4.9 40.0 1.0 CE1 A:HIS10 5.0 47.9 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