Sodium in PDB 5w8s: Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations

All present enzymatic activity of Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations:
2.4.1.182;

The structure of Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations, PDB code: 5w8s 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)	55.07 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.016, 68.016, 155.139, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 22.3

The binding sites of Sodium atom in the Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations (pdb code 5w8s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations, PDB code: 5w8s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:52.1 occ:1.00 H A:LEU328 2.1 49.4 1.0 OE1 A:GLU331 2.4 54.3 1.0 HA A:LEU327 2.7 46.3 1.0 N A:LEU328 2.9 41.2 1.0 O A:GLU326 3.1 42.7 1.0 HG A:LEU328 3.1 51.8 1.0 HB2 A:LEU328 3.2 51.0 1.0 HH12 A:ARG129 3.4 75.9 1.0 HB2 A:GLU331 3.4 50.9 1.0 CA A:LEU327 3.5 38.6 1.0 CD A:GLU331 3.6 52.7 1.0 C A:LEU327 3.7 38.2 1.0 CB A:LEU328 3.7 42.5 1.0 CA A:LEU328 3.8 42.9 1.0 CG A:LEU328 3.8 43.1 1.0 HD23 A:LEU327 3.8 59.7 1.0 C A:GLU326 3.9 40.7 1.0 NH1 A:ARG129 3.9 63.3 1.0 O A:HOH576 3.9 54.2 1.0 O A:LEU328 4.0 37.4 1.0 HD12 A:LEU328 4.0 57.2 1.0 HB3 A:GLU331 4.1 50.9 1.0 N A:LEU327 4.1 38.2 1.0 CB A:GLU331 4.1 42.4 1.0 HH11 A:ARG129 4.1 75.9 1.0 HH2 A:TRP128 4.3 54.9 1.0 C A:LEU328 4.4 39.1 1.0 CG A:GLU331 4.4 49.8 1.0 OE2 A:GLU331 4.5 58.2 1.0 CD1 A:LEU328 4.5 47.7 1.0 HH22 A:ARG129 4.6 75.3 1.0 HA A:LEU328 4.6 51.4 1.0 HB3 A:LEU328 4.7 51.0 1.0 O A:HOH524 4.7 57.9 1.0 HG3 A:GLU331 4.7 59.8 1.0 CD2 A:LEU327 4.7 49.8 1.0 CB A:LEU327 4.8 36.6 1.0 CZ A:ARG129 4.8 61.5 1.0 HB2 A:GLU326 4.8 48.1 1.0 HB3 A:LEU327 4.8 43.9 1.0 HZ2 A:TRP128 4.8 57.1 1.0 H A:LEU327 4.8 45.9 1.0 HD22 A:LEU327 4.9 59.7 1.0 O A:LEU327 4.9 37.5 1.0 HD11 A:LEU328 4.9 57.2 1.0 NH2 A:ARG129 5.0 62.7 1.0 HB3 A:GLU326 5.0 48.1 1.0

Sodium binding site 2 out of 2 in the Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lipid A Disaccharide Synthase (Lpxb)-7 Solubilizing Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:63.3 occ:1.00 OE2 A:GLU227 2.4 51.2 1.0 HB3 A:ASP225 3.1 55.6 1.0 O A:ASP225 3.2 41.0 1.0 HG2 A:GLU227 3.2 57.6 1.0 HB2 A:ALA191 3.2 67.2 1.0 CD A:GLU227 3.3 49.7 1.0 HB1 A:ALA191 3.4 67.2 1.0 HG3 A:PRO188 3.5 59.8 1.0 HG2 A:PRO188 3.7 59.8 1.0 CG A:GLU227 3.7 48.0 1.0 CB A:ALA191 3.7 56.0 1.0 O A:HOH610 3.8 49.6 1.0 HG3 A:GLU227 4.0 57.6 1.0 HB3 A:ALA191 4.0 67.2 1.0 CB A:ASP225 4.0 46.3 1.0 CG A:PRO188 4.0 49.8 1.0 C A:ASP225 4.1 44.6 1.0 OE1 A:GLU227 4.4 49.4 1.0 HA A:ASP225 4.4 56.0 1.0 CA A:ASP225 4.5 46.6 1.0 HB2 A:ASP225 4.6 55.6 1.0 HD2 A:PRO188 4.6 52.6 1.0 CG A:ASP225 4.8 51.8 1.0 CD A:PRO188 4.8 43.9 1.0

T.E.Bohl, K.Shi, J.K.Lee, H.Aihara. Crystal Structure of Lipid A Disaccharide Synthase Lpxb From Escherichia Coli. Nat Commun V. 9 377 2018.
ISSN: ESSN 2041-1723
PubMed: 29371662
DOI: 10.1038/S41467-017-02712-9