Manganese in PDB 6pj3: Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex

All present enzymatic activity of Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex:
3.6.1.54;

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex, PDB code: 6pj3 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)	45.81 / 2.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.800, 105.800, 53.440, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 21.5

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Manganese atom in the Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex (pdb code 6pj3). 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 the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex, PDB code: 6pj3:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex


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 the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:45.9 occ:1.00 OD1 A:ASP8 2.0 31.1 1.0 NE2 A:HIS10 2.3 33.4 1.0 NE2 A:HIS197 2.3 40.0 1.0 O A:HOH443 2.4 51.2 1.0 OD2 A:ASP41 2.5 33.1 1.0 CE1 A:HIS10 2.8 37.8 1.0 CG A:ASP8 2.9 35.7 1.0 CE1 A:HIS197 3.2 36.5 1.0 CD2 A:HIS197 3.3 35.2 1.0 CB A:ASP8 3.3 26.5 1.0 CG A:ASP41 3.5 28.6 1.0 MN A:MN302 3.5 84.9 1.0 CD2 A:HIS10 3.5 30.6 1.0 CB A:ASP41 3.7 26.6 1.0 O A:HOH482 3.7 42.6 1.0 CA A:ASP8 3.9 29.9 1.0 OD2 A:ASP8 4.0 35.9 1.0 ND1 A:HIS10 4.0 37.1 1.0 O A:HIS195 4.1 34.4 1.0 CA A:HIS195 4.4 28.3 1.0 ND1 A:HIS197 4.4 43.9 1.0 CG A:HIS10 4.4 30.5 1.0 CG A:HIS197 4.4 37.6 1.0 OD1 A:ASP41 4.6 23.6 1.0 C A:HIS195 4.7 36.8 1.0 CE1 A:HIS114 4.7 28.0 1.0 OD1 A:ASN79 4.8 39.9 1.0 C A:ASP8 4.8 35.3 1.0 NE2 A:HIS114 4.9 32.4 1.0 N A:HIS195 4.9 29.9 1.0 N A:ASP8 4.9 26.1 1.0 O A:ASP8 5.0 28.0 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex


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 the Klebsiella Pneumoniae Lpxh/Jh-Lph-33 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:84.9 occ:1.00 OD1 A:ASN79 2.0 39.9 1.0 NE2 A:HIS114 2.2 32.4 1.0 ND1 A:HIS195 2.3 33.4 1.0 OD2 A:ASP41 2.3 33.1 1.0 O A:HOH443 2.8 51.2 1.0 CE1 A:HIS114 3.0 28.0 1.0 CG A:ASP41 3.2 28.6 1.0 CG A:ASN79 3.2 30.5 1.0 CG A:HIS195 3.2 29.4 1.0 CE1 A:HIS195 3.2 35.2 1.0 CD2 A:HIS114 3.3 26.7 1.0 CB A:HIS195 3.4 21.7 1.0 CA A:HIS195 3.5 28.3 1.0 MN A:MN301 3.5 45.9 1.0 OD1 A:ASP41 3.6 23.6 1.0 OD1 A:ASP8 3.6 31.1 1.0 O A:HOH482 3.9 42.6 1.0 ND2 A:ASN79 3.9 34.1 1.0 O A:HIS195 4.1 34.4 1.0 ND1 A:HIS114 4.2 27.6 1.0 N A:ASN79 4.2 35.1 1.0 CB A:ASN79 4.3 27.2 1.0 C A:HIS195 4.3 36.8 1.0 CB A:ASP41 4.3 26.6 1.0 NE2 A:HIS195 4.4 34.7 1.0 CD2 A:HIS195 4.4 40.8 1.0 CG A:HIS114 4.4 28.9 1.0 N A:HIS195 4.5 29.9 1.0 CG A:ASP8 4.8 35.7 1.0 CA A:ASN79 4.8 35.3 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