Sodium in PDB 9h0n: Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Galacto-N-Biose

The structure of Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Galacto-N-Biose, PDB code: 9h0n 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)	43.41 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.1, 53.25, 149.92, 90, 90, 90
R / Rfree (%)	16.8 / 19.3

The binding sites of Sodium atom in the Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Galacto-N-Biose (pdb code 9h0n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Galacto-N-Biose, PDB code: 9h0n:

Sodium binding site 1 out of 1 in the Fucosylated Lacto-N-Biose Binding Protein From Bifidobacterium Longum Subsp. Infantis in Complex with Galacto-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 Galacto-N-Biose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:54.2 occ:1.00 O A:ASP371 2.2 29.3 1.0 O A:HOH974 2.3 43.1 1.0 O A:HOH900 2.6 37.7 1.0 O A:ASN369 3.3 29.2 1.0 C A:ASP371 3.4 26.1 1.0 O A:ASP372 3.5 24.0 1.0 C A:ASP372 3.6 22.5 1.0 C A:ASN369 3.7 27.8 1.0 N A:LEU373 4.0 22.5 1.0 N A:ASP371 4.0 20.9 1.0 O A:GLY368 4.1 22.7 1.0 CA A:ASN369 4.2 23.6 1.0 OD1 A:ASN369 4.2 26.7 1.0 N A:ASP372 4.2 28.0 1.0 CA A:ASP372 4.2 23.8 1.0 CB A:ASP372 4.3 23.7 1.0 N A:THR370 4.3 27.4 1.0 CA A:LEU373 4.3 22.9 1.0 CA A:ASP371 4.4 21.8 1.0 C A:THR370 4.4 29.2 1.0 CA A:THR370 4.4 29.5 1.0 O A:HOH922 4.5 25.2 1.0 O A:HOH745 4.6 31.1 1.0 O A:HOH1101 5.0 41.3 1.0 CG A:ASN369 5.0 25.9 1.0 CD2 A:LEU373 5.0 24.9 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