Sodium in PDB 8yk2: Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct T7-TAG_24-700

The structure of Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct T7-TAG_24-700, PDB code: 8yk2 was solved by T.Kashima, M.Akama, H.Ashida, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.80 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.557, 125.055, 196.788, 90, 90, 90
R / Rfree (%)	18 / 21.2

The binding sites of Sodium atom in the Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct T7-TAG_24-700 (pdb code 8yk2). 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 Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct T7-TAG_24-700, PDB code: 8yk2:

Sodium binding site 1 out of 1 in the Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct T7-TAG_24-700


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct T7-TAG_24-700 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1302 b:44.1 occ:1.00 O A:HOH1783 3.7 41.1 1.0 ND2 A:ASN112 3.7 28.3 1.0 NZ A:LYS111 3.9 41.7 1.0 CD A:LYS111 4.2 33.1 1.0 NH2 A:ARG137 4.3 47.1 1.0 CE A:LYS111 4.4 35.8 1.0 NE A:ARG137 4.6 42.5 1.0 CG A:ASN112 4.8 29.0 1.0 CZ A:ARG137 4.9 45.3 1.0 OD1 A:ASN112 5.0 27.8 1.0

T.Kashima, M.Akama, T.Wakinaka, T.Arakawa, H.Ashida, S.Fushinobu. Crystal Structure of Bifidobacterium Bifidum Glycoside Hydrolase Family 110 Alpha-Galactosidase Specific For Blood Group B Antigen J.Appl.Glyosci. 2024.
ISSN: ISSN 1344-7882
DOI: 10.5458/JAG.JAG.JAG-2024_0005