Sodium in PDB 9h0o: Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose

The structure of Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose, PDB code: 9h0o was solved by M.Jensen, M.E.Hansen, H.Sakanaka, D.J.Slotboom, M.Abou Hachem, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.58 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.07, 52.56, 149.319, 90, 90, 90
R / Rfree (%)	20.2 / 23.6

The structure of Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose (pdb code 9h0o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose, PDB code: 9h0o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:41.9 occ:1.00 O A:GLY361 2.4 33.4 1.0 O A:HOH706 2.7 33.9 1.0 OG1 A:THR289 2.7 41.0 1.0 OH A:TYR381 2.9 41.1 1.0 CG1 A:ILE363 3.4 33.7 1.0 CB A:THR289 3.6 37.8 1.0 OH A:TYR48 3.6 35.7 1.0 C A:GLY361 3.7 37.7 1.0 CB A:ILE363 3.8 36.7 1.0 CG2 A:THR289 3.9 38.9 1.0 N A:ILE363 3.9 37.8 1.0 SD A:MET377 3.9 41.6 1.0 CZ A:TYR381 3.9 43.4 1.0 CE1 A:TYR381 4.1 43.9 1.0 CA A:SER161 4.2 45.2 1.0 CB A:SER161 4.2 46.2 1.0 O A:TYR160 4.4 37.0 1.0 CZ A:TYR48 4.5 37.6 1.0 CA A:ILE363 4.5 37.4 1.0 CA A:GLY361 4.5 36.2 1.0 OG A:SER161 4.5 50.4 1.0 CA A:ALA362 4.6 39.5 1.0 N A:ALA362 4.6 38.3 1.0 C A:ALA362 4.6 35.4 1.0 CD1 A:ILE363 4.6 39.2 1.0 N A:SER161 4.7 47.0 1.0 CE1 A:TYR48 4.7 32.0 1.0 C A:TYR160 4.7 43.7 1.0 CD A:PRO162 4.9 41.8 1.0 CG A:MET377 5.0 40.6 1.0 CA A:THR289 5.0 36.8 1.0

Sodium binding site 2 out of 2 in the Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Lacto-N-Biose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:47.5 occ:1.00 O A:HOH858 2.5 43.3 1.0 OD2 A:ASP376 2.8 37.8 1.0 O A:HOH690 2.9 35.0 1.0 O A:THR360 3.2 40.9 1.0 O A:HOH685 3.2 34.0 1.0 C A:THR360 3.4 36.7 1.0 CG A:ASP376 3.7 39.6 1.0 CE A:MET377 3.8 36.4 1.0 N A:GLY361 3.9 38.3 1.0 CG1 A:VAL292 4.0 36.0 1.0 CA A:THR360 4.1 36.0 1.0 CB A:ASN293 4.1 35.3 1.0 OD1 A:ASP376 4.1 45.8 1.0 CA A:GLY361 4.1 36.2 1.0 CB A:VAL292 4.1 40.4 1.0 N A:ASN293 4.1 38.9 1.0 O A:HOH944 4.2 43.1 1.0 O A:HOH689 4.3 45.2 1.0 CA A:ASN293 4.5 42.0 1.0 O A:HOH693 4.6 37.6 1.0 CB A:ASP376 4.8 43.2 1.0 O A:LYS359 4.8 40.1 1.0 C A:VAL292 4.8 41.7 1.0 O A:HOH842 4.9 45.0 1.0

M.E.Hansen, M.Sakanaka, M.Jensen, H.Sakanaka, M.J.Pichler, S.Maeda, J.F.Hoevring, A.Nakajima, S.Kunstmann, T.S.Nielsen, G.H.J.Peters, D.J.Slotboom, J.P.Morth, T.Katayama, M.Abou Hachem. Uptake of Fucosylated Type I Human Milk Oligosaccharide Blocks By Bifidobacterium Longum Subsp. Infantis Mbio 2025.
ISSN: ESSN 2150-7511
DOI: 10.1128/MBIO.00368-25