Manganese in PDB 5k8k: Structure of the Haemophilus Influenzae Lpxh-Lipid X Complex

All present enzymatic activity of Structure of the Haemophilus Influenzae Lpxh-Lipid X Complex:
3.6.1.54;

The structure of Structure of the Haemophilus Influenzae Lpxh-Lipid X Complex, PDB code: 5k8k was solved by J.Cho, C.-J.Lee, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.42 / 2.55
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	99.840, 99.840, 200.850, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.7

The binding sites of Manganese atom in the Structure of the Haemophilus Influenzae Lpxh-Lipid X Complex (pdb code 5k8k). 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 Haemophilus Influenzae Lpxh-Lipid X Complex, PDB code: 5k8k:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of the Haemophilus Influenzae Lpxh-Lipid X 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 Haemophilus Influenzae Lpxh-Lipid X Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:56.5 occ:0.86 OD1 A:ASN80 2.0 45.8 1.0 ND1 A:HIS196 2.1 54.9 1.0 OD2 A:ASP42 2.1 51.9 1.0 NE2 A:HIS115 2.3 43.9 1.0 CG A:HIS196 3.0 51.0 1.0 CG A:ASN80 3.1 50.7 1.0 MN A:MN302 3.1 86.9 0.6 CE1 A:HIS196 3.1 54.7 1.0 CE1 A:HIS115 3.1 40.5 1.0 CG A:ASP42 3.2 48.2 1.0 CB A:HIS196 3.3 48.0 1.0 CD2 A:HIS115 3.4 40.7 1.0 CA A:HIS196 3.4 48.8 1.0 ND2 A:ASN80 3.5 51.0 1.0 OD1 A:ASP9 3.6 63.9 1.0 OD1 A:ASP42 3.7 47.4 1.0 CD2 A:HIS196 4.2 51.0 1.0 O A:HIS196 4.2 57.4 1.0 NE2 A:HIS196 4.2 52.4 1.0 C A:HIS196 4.3 55.6 1.0 ND1 A:HIS115 4.3 40.9 1.0 O48 A:LP5303 4.3 66.0 1.0 N A:HIS196 4.4 45.0 1.0 CB A:ASN80 4.4 50.4 1.0 CG A:HIS115 4.4 40.0 1.0 N A:ASN80 4.4 46.3 1.0 CB A:ASP42 4.5 47.8 1.0 CG A:ASP9 4.5 57.3 1.0 OD2 A:ASP9 4.6 56.2 1.0

Manganese binding site 2 out of 2 in the Structure of the Haemophilus Influenzae Lpxh-Lipid X 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 Haemophilus Influenzae Lpxh-Lipid X Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:86.9 occ:0.55 OD1 A:ASP9 2.2 63.9 1.0 NE2 A:HIS11 2.3 60.7 1.0 OD2 A:ASP42 2.3 51.9 1.0 MN A:MN301 3.1 56.5 0.9 CE1 A:HIS11 3.2 63.3 1.0 CG A:ASP42 3.3 48.2 1.0 CD2 A:HIS11 3.4 61.4 1.0 CG A:ASP9 3.4 57.3 1.0 CE1 A:HIS198 3.5 77.8 1.0 CB A:ASP42 3.8 47.8 1.0 O48 A:LP5303 3.9 66.0 1.0 ND1 A:HIS198 4.1 77.0 1.0 CB A:ASP9 4.2 52.6 1.0 O A:HIS196 4.3 57.4 1.0 OD1 A:ASP42 4.3 47.4 1.0 OD2 A:ASP9 4.3 56.2 1.0 ND1 A:HIS11 4.4 67.8 1.0 CG A:HIS11 4.5 65.1 1.0 OD1 A:ASN80 4.5 45.8 1.0 NE2 A:HIS198 4.5 81.3 1.0 CA A:HIS196 4.5 48.8 1.0 OD1 A:ASP215 4.6 67.5 1.0 CA A:ASP9 4.6 48.9 1.0 ND1 A:HIS196 4.6 54.9 1.0 NH2 A:ARG81 4.7 64.4 1.0 CG A:ARG81 4.7 48.5 1.0 NE A:ARG81 4.7 59.3 1.0 CZ A:ARG81 4.7 61.7 1.0 ND2 A:ASN80 4.8 51.0 1.0 NE2 A:HIS115 4.9 43.9 1.0 C A:HIS196 4.9 55.6 1.0 CE1 A:HIS115 5.0 40.5 1.0

J.Cho, C.J.Lee, J.Zhao, H.E.Young, P.Zhou. Structure of the Essential Haemophilus Influenzae Udp-Diacylglucosamine Pyrophosphohydrolase Lpxh in Lipid A Biosynthesis. Nat Microbiol V. 1 16154 2016.
ISSN: ESSN 2058-5276
PubMed: 27780190
DOI: 10.1038/NMICROBIOL.2016.154