Sodium in PDB 8yk1: Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844

The structure of Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844, PDB code: 8yk1 was solved by T.Kashima, H.Ashida, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.59 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.689, 68.771, 291.306, 90, 91.4, 90
R / Rfree (%)	18.9 / 22.1

The binding sites of Sodium atom in the Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844 (pdb code 8yk1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844, PDB code: 8yk1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844


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 23-844 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:14.1 occ:1.00 NZ A:LYS102 3.7 22.8 1.0 CG A:PRO78 4.0 15.4 1.0 CB A:PRO78 4.1 17.0 1.0 CA A:ASP79 4.2 17.6 1.0 CE1 A:TYR199 4.2 16.8 1.0 N A:ASP79 4.3 18.4 1.0 O A:HOH1289 4.3 17.3 1.0 C A:PRO78 4.4 16.6 1.0 CD1 A:TYR199 4.6 14.8 1.0 CG A:ASP79 4.6 19.8 1.0 O A:PRO78 4.6 17.6 1.0 OD1 A:ASP79 4.7 18.6 1.0 OD2 A:ASP79 4.8 23.9 1.0 CE A:LYS102 4.9 24.8 1.0 CA A:PRO78 4.9 16.7 1.0 CB A:ASP79 5.0 19.8 1.0

Sodium binding site 2 out of 3 in the Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:3.8 occ:1.00 CG B:PRO78 3.8 18.6 1.0 CB B:PRO78 4.1 19.2 1.0 CE1 B:TYR199 4.2 18.8 1.0 CA B:ASP79 4.2 20.2 1.0 N B:ASP79 4.3 16.7 1.0 O B:HOH1290 4.3 21.9 1.0 C B:PRO78 4.4 20.7 1.0 CD1 B:TYR199 4.4 18.4 1.0 CG B:ASP79 4.5 21.2 1.0 NZ B:LYS102 4.6 28.7 1.0 OD1 B:ASP79 4.6 19.6 1.0 O B:PRO78 4.6 18.5 1.0 OD2 B:ASP79 4.7 20.7 1.0 CA B:PRO78 4.9 18.6 1.0 O B:HOH1349 4.9 38.9 1.0 CB B:ASP79 4.9 22.3 1.0

Sodium binding site 3 out of 3 in the Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Blood Group B Alpha-1,3-Galactosidase Agabb From Bifidobacterium Bifidum, Construct 23-844 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na901 b:3.8 occ:1.00 CG C:PRO78 3.9 19.3 1.0 NZ C:LYS102 4.0 31.9 1.0 CB C:PRO78 4.1 19.8 1.0 CE1 C:TYR199 4.1 17.3 1.0 CA C:ASP79 4.2 21.4 1.0 O C:HOH1179 4.2 19.2 1.0 N C:ASP79 4.2 19.7 1.0 C C:PRO78 4.4 19.4 1.0 CG C:ASP79 4.4 21.6 1.0 OD1 C:ASP79 4.4 20.9 1.0 CD1 C:TYR199 4.5 17.2 1.0 OD2 C:ASP79 4.6 22.2 1.0 O C:PRO78 4.6 18.6 1.0 CB C:ASP79 4.8 22.0 1.0 CA C:PRO78 4.9 21.0 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