Manganese in PDB 6pib: Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex

All present enzymatic activity of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex:
3.6.1.54;

The structure of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex, PDB code: 6pib was solved by J.Cho, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.96 / 2.26
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.750, 106.750, 52.970, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.9

The structure of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Manganese atom in the Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex (pdb code 6pib). 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 the Klebsiella Pneumoniae Lpxh-AZ1 Complex, PDB code: 6pib:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:55.8 occ:1.00 OD1 A:ASP8 1.9 57.5 1.0 O A:HOH409 2.1 54.3 1.0 NE2 A:HIS197 2.2 64.7 1.0 NE2 A:HIS10 2.3 54.1 1.0 CG A:ASP8 2.7 44.2 1.0 OD2 A:ASP41 2.7 53.0 1.0 CB A:ASP8 3.1 40.7 1.0 CE1 A:HIS10 3.2 49.0 1.0 CD2 A:HIS197 3.2 58.7 1.0 CE1 A:HIS197 3.2 64.7 1.0 CD2 A:HIS10 3.3 46.3 1.0 MN A:MN302 3.5 58.6 1.0 CG A:ASP41 3.6 45.0 1.0 CA A:ASP8 3.7 46.9 1.0 OD2 A:ASP8 3.7 56.8 1.0 CB A:ASP41 3.7 47.7 1.0 O A:HOH440 3.8 51.9 1.0 O A:HIS195 4.1 53.0 1.0 CA A:HIS195 4.3 47.1 1.0 ND1 A:HIS10 4.3 51.7 1.0 ND1 A:HIS197 4.3 69.3 1.0 CG A:HIS197 4.4 62.8 1.0 CG A:HIS10 4.4 48.8 1.0 C A:HIS195 4.6 51.3 1.0 C A:ASP8 4.6 43.7 1.0 CE1 A:HIS114 4.7 45.7 1.0 N A:HIS195 4.7 47.0 1.0 N A:ASP8 4.8 41.5 1.0 OD1 A:ASP41 4.8 42.2 1.0 O A:ASP8 4.8 45.4 1.0 NE2 A:HIS114 4.9 43.3 1.0

Manganese binding site 2 out of 2 in the Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Klebsiella Pneumoniae Lpxh-AZ1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:58.6 occ:1.00 OD1 A:ASN79 1.9 58.0 1.0 O A:HOH409 2.1 54.3 1.0 OD2 A:ASP41 2.1 53.0 1.0 NE2 A:HIS114 2.3 43.3 1.0 ND1 A:HIS195 2.3 52.7 1.0 CE1 A:HIS114 3.0 45.7 1.0 CG A:ASN79 3.0 50.0 1.0 CG A:ASP41 3.1 45.0 1.0 CE1 A:HIS195 3.3 54.5 1.0 CG A:HIS195 3.3 56.4 1.0 CD2 A:HIS114 3.4 43.6 1.0 OD1 A:ASP8 3.5 57.5 1.0 MN A:MN301 3.5 55.8 1.0 CA A:HIS195 3.5 47.1 1.0 OD1 A:ASP41 3.5 42.2 1.0 CB A:HIS195 3.6 42.9 1.0 ND2 A:ASN79 3.6 45.8 1.0 O A:HOH440 3.7 51.9 1.0 O A:HIS195 4.2 53.0 1.0 ND1 A:HIS114 4.2 46.5 1.0 CB A:ASP41 4.3 47.7 1.0 CB A:ASN79 4.3 45.0 1.0 N A:ASN79 4.3 50.6 1.0 C A:HIS195 4.3 51.3 1.0 NE2 A:HIS195 4.4 61.2 1.0 CD2 A:HIS195 4.4 50.2 1.0 CG A:HIS114 4.4 44.2 1.0 N A:HIS195 4.5 47.0 1.0 CG A:ASP8 4.6 44.2 1.0 CA A:ASN79 4.9 50.4 1.0

J.Cho, M.Lee, C.Cochrane, C.Webster, B.Fenton, J.Zhao, J.Hong, P.Zhao. Structural Basis of the Udp-Diacylglucosamine Pyrophosphohydrolase Lpxh Inhibition By Sulfonyl Piperazine Antibiotics Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1912876117