Sodium in PDB 6e57: Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-B in Complex with Mixed-Linkage Heptasaccharide

The structure of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-B in Complex with Mixed-Linkage Heptasaccharide, PDB code: 6e57 was solved by N.M.Koropatkin, M.Schnizlein, C.M.E.Bahr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.34 / 2.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	156.438, 243.652, 76.059, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.8

The binding sites of Sodium atom in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-B in Complex with Mixed-Linkage Heptasaccharide (pdb code 6e57). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-B in Complex with Mixed-Linkage Heptasaccharide, PDB code: 6e57:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-B in Complex with Mixed-Linkage Heptasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-B in Complex with Mixed-Linkage Heptasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:59.0 occ:1.00 O A:GLY155 2.5 41.5 1.0 OE2 A:GLU182 3.0 50.3 1.0 O3 A:PO4511 3.4 86.9 1.0 O3 A:PO4508 3.4 65.1 1.0 O A:HOH617 3.6 51.0 1.0 C A:GLY155 3.7 41.8 1.0 CD A:GLU182 3.9 50.0 1.0 CG A:GLU182 4.1 49.2 1.0 O1 A:PO4508 4.2 61.7 1.0 OG A:SER156 4.2 45.8 1.0 P A:PO4508 4.3 61.9 1.0 P A:PO4511 4.4 91.3 1.0 CA A:SER156 4.6 44.5 1.0 N A:SER156 4.6 43.8 1.0 O4 A:PO4508 4.6 63.9 1.0 O1 A:PO4511 4.6 82.8 1.0 CA A:GLY155 4.7 41.2 1.0 O2 A:PO4511 4.7 82.8 1.0 N A:GLY155 4.9 40.2 1.0 CB A:SER156 4.9 45.2 1.0

Sodium binding site 2 out of 2 in the Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-B in Complex with Mixed-Linkage Heptasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacteroides Ovatus Mixed-Linkage Glucan Utilization Locus (Mlgul) Sgbp-B in Complex with Mixed-Linkage Heptasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na510 b:54.9 occ:1.00 O C:HOH614 2.3 42.0 1.0 O C:GLY156 2.8 36.8 1.0 OE2 C:GLU183 3.2 52.4 1.0 O1 C:PO4507 3.5 89.6 1.0 O4 C:PO4507 3.7 76.1 1.0 C C:GLY156 3.9 35.8 1.0 CD C:GLU183 4.1 53.9 1.0 CG C:GLU183 4.2 50.9 1.0 P C:PO4507 4.2 90.5 1.0 OG C:SER157 4.2 41.6 1.0 O3 C:PO4506 4.5 50.7 1.0 O4 C:PO4506 4.7 51.4 1.0 CA C:GLY156 4.8 35.0 1.0 N C:SER157 4.8 35.2 1.0 O1 C:PO4506 4.8 43.9 1.0 CA C:SER157 4.8 36.1 1.0 O2 C:PO4507 4.8 76.4 1.0 O C:HOH617 4.8 38.8 1.0 P C:PO4506 4.9 48.5 1.0

K.Tamura, M.H.Foley, B.R.Gardill, G.Dejean, M.Schnizlein, C.M.E.Bahr, A.Louise Creagh, F.Van Petegem, N.M.Koropatkin, H.Brumer. Surface Glycan-Binding Proteins Are Essential For Cereal Beta-Glucan Utilization By the Human Gut Symbiont Bacteroides Ovatus. Cell.Mol.Life Sci. V. 76 4319 2019.
ISSN: ESSN 1420-9071
PubMed: 31062073
DOI: 10.1007/S00018-019-03115-3