Manganese in PDB 5wly: E. Coli Lpxh- 8 Mutations

All present enzymatic activity of E. Coli Lpxh- 8 Mutations:
3.6.1.54;

The structure of E. Coli Lpxh- 8 Mutations, PDB code: 5wly was solved by T.E.Bohl, H.Aihara, K.Shi, J.K.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.23 / 2.00
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	57.012, 62.064, 66.047, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.7

The structure of E. Coli Lpxh- 8 Mutations also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the E. Coli Lpxh- 8 Mutations (pdb code 5wly). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the E. Coli Lpxh- 8 Mutations, PDB code: 5wly:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the E. Coli Lpxh- 8 Mutations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of E. Coli Lpxh- 8 Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:32.3 occ:1.00 O A:HOH411 2.1 19.4 1.0 OD1 A:ASN79 2.1 36.0 1.0 OD2 A:ASP41 2.1 35.2 1.0 NE2 A:HIS114 2.1 32.2 1.0 ND1 A:HIS195 2.2 29.4 1.0 HA A:HIS195 2.8 37.6 1.0 CE1 A:HIS114 3.0 26.8 1.0 HE1 A:HIS114 3.1 31.6 1.0 CG A:ASP41 3.1 27.7 1.0 CE1 A:HIS195 3.1 32.7 1.0 CG A:ASN79 3.2 30.6 1.0 CD2 A:HIS114 3.2 27.9 1.0 CG A:HIS195 3.3 30.5 1.0 HE1 A:HIS195 3.3 40.0 1.0 O A:HOH481 3.3 30.5 1.0 MN A:MN302 3.3 31.4 1.0 HD21 A:ASN79 3.4 36.5 1.0 HB2 A:HIS195 3.4 37.3 1.0 H A:ASN79 3.5 30.0 1.0 HD2 A:HIS114 3.5 33.7 1.0 OD1 A:ASP41 3.5 21.2 1.0 CA A:HIS195 3.6 30.8 1.0 CB A:HIS195 3.6 30.5 1.0 ND2 A:ASN79 3.7 29.8 1.0 OD1 A:ASP8 3.9 33.7 1.0 HB3 A:ASP116 4.0 41.5 1.0 HG2 A:ARG80 4.1 35.2 1.0 O A:HIS195 4.1 32.3 1.0 ND1 A:HIS114 4.1 27.6 1.0 NE2 A:HIS195 4.3 33.4 1.0 N A:ASN79 4.3 24.5 1.0 CG A:HIS114 4.3 26.8 1.0 HB2 A:ASP41 4.3 28.5 1.0 CB A:ASP41 4.3 23.2 1.0 C A:HIS195 4.3 32.6 1.0 CD2 A:HIS195 4.4 33.5 1.0 CB A:ASN79 4.4 28.5 1.0 HD22 A:ASN79 4.5 36.5 1.0 HE1 A:HIS10 4.5 46.1 1.0 HB3 A:HIS195 4.6 37.3 1.0 H A:HIS195 4.6 33.7 1.0 HB3 A:ASN79 4.6 34.9 1.0 N A:HIS195 4.6 27.5 1.0 HA3 A:GLY78 4.6 29.4 1.0 H A:ARG80 4.6 27.3 1.0 HB3 A:ASP41 4.7 28.5 1.0 NE2 A:HIS197 4.9 38.4 1.0 HD1 A:HIS114 4.9 33.8 1.0 CA A:ASN79 4.9 24.9 1.0 CB A:ASP116 5.0 34.0 1.0

Manganese binding site 2 out of 2 in the E. Coli Lpxh- 8 Mutations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of E. Coli Lpxh- 8 Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:31.4 occ:1.00 O A:HOH411 1.9 19.4 1.0 OD1 A:ASP8 2.1 33.7 1.0 NE2 A:HIS197 2.2 38.4 1.0 NE2 A:HIS10 2.2 40.4 1.0 OD2 A:ASP41 2.3 35.2 1.0 HE1 A:HIS10 2.6 46.1 1.0 CE1 A:HIS10 2.7 37.9 1.0 CE1 A:HIS197 3.0 36.4 1.0 HE1 A:HIS197 3.0 44.3 1.0 CG A:ASP8 3.1 30.8 1.0 HB3 A:ASP41 3.1 28.5 1.0 CG A:ASP41 3.2 27.7 1.0 CD2 A:HIS197 3.3 35.3 1.0 MN A:MN301 3.3 32.3 1.0 HB3 A:ASP8 3.4 36.2 1.0 HB2 A:ASP41 3.4 28.5 1.0 HA A:HIS195 3.4 37.6 1.0 CB A:ASP41 3.5 23.2 1.0 CD2 A:HIS10 3.5 36.8 1.0 HA A:ASP8 3.5 32.0 1.0 HD2 A:HIS197 3.6 43.0 1.0 HE1 A:HIS114 3.6 31.6 1.0 CB A:ASP8 3.7 29.6 1.0 O A:HOH481 3.8 30.5 1.0 HD2 A:HIS10 3.9 44.9 1.0 ND1 A:HIS10 4.0 36.6 1.0 O A:HIS195 4.1 32.3 1.0 OD2 A:ASP8 4.1 31.5 1.0 CA A:ASP8 4.1 26.1 1.0 ND1 A:HIS197 4.2 38.0 1.0 CA A:HIS195 4.3 30.8 1.0 CE1 A:HIS114 4.3 26.8 1.0 CG A:HIS197 4.3 37.4 1.0 CG A:HIS10 4.4 35.2 1.0 OD1 A:ASP41 4.4 21.2 1.0 H A:HIS195 4.4 33.7 1.0 NE2 A:HIS114 4.5 32.2 1.0 HG2 A:ARG80 4.5 35.2 1.0 HB2 A:ASP8 4.6 36.2 1.0 C A:HIS195 4.6 32.6 1.0 HD1 A:HIS10 4.7 44.6 1.0 HG3 A:ARG80 4.8 35.2 1.0 N A:HIS195 4.9 27.5 1.0 HD1 A:HIS197 4.9 46.3 1.0 ND1 A:HIS195 4.9 29.4 1.0 HB2 A:ALA218 4.9 42.1 1.0 CA A:ASP41 5.0 21.1 1.0

T.E.Bohl, P.Ieong, J.K.Lee, T.Lee, J.Kankanala, K.Shi, O.Demir, K.Kurahashi, R.E.Amaro, Z.Wang, H.Aihara. The Substrate-Binding Cap of the Udp-Diacylglucosamine Pyrophosphatase Lpxh Is Highly Flexible, Enabling Facile Substrate Binding and Product Release. J. Biol. Chem. V. 293 7969 2018.
ISSN: ESSN 1083-351X
PubMed: 29626094
DOI: 10.1074/JBC.RA118.002503