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

Enzymatic activity of 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;

Protein crystallography data

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

Sodium Binding Sites:

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 5w8s

Go back to Sodium Binding Sites List in 5w8s
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 5w8s

Go back to Sodium Binding Sites List in 5w8s
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

Reference:

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
Page generated: Tue Oct 8 01:00:44 2024

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