Sodium in PDB 7xsh: Crystal Structure of CLAGL29B Bound with L-Glucose

The structure of Crystal Structure of CLAGL29B Bound with L-Glucose, PDB code: 7xsh was solved by R.Shishiuchi, H.Kang, T.Tagami, M.Okuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.60 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.393, 121.583, 166.372, 90, 90, 90
R / Rfree (%)	17.9 / 20.2

The binding sites of Sodium atom in the Crystal Structure of CLAGL29B Bound with L-Glucose (pdb code 7xsh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of CLAGL29B Bound with L-Glucose, PDB code: 7xsh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of CLAGL29B Bound with L-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of CLAGL29B Bound with L-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:34.1 occ:1.00 O A:HOH942 2.3 37.0 1.0 O A:HIS98 2.4 22.8 1.0 O A:LYS96 2.4 25.3 1.0 O A:HOH841 2.5 27.8 1.0 O A:HOH846 2.7 22.2 1.0 C A:LYS96 3.4 23.6 1.0 C A:HIS98 3.6 21.3 1.0 CA A:LYS96 3.9 23.3 1.0 OD1 A:ASP398 4.1 18.2 1.0 N A:HIS98 4.2 21.1 1.0 O A:LEU95 4.3 18.9 1.0 N A:LEU97 4.4 22.7 1.0 C A:LEU97 4.5 23.3 1.0 CA A:HIS98 4.5 20.5 1.0 CG A:LYS96 4.5 33.1 1.0 N A:GLU99 4.5 23.0 1.0 CA A:GLU99 4.6 24.1 1.0 CB A:LYS96 4.8 26.6 1.0 O A:GLY397 4.8 17.4 1.0 CA A:LEU97 4.8 24.0 1.0 N A:LYS96 5.0 19.5 1.0 O A:LEU97 5.0 23.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of CLAGL29B Bound with L-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of CLAGL29B Bound with L-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:23.6 occ:1.00 O B:HOH1037 2.2 31.1 1.0 O B:HOH1031 2.4 28.4 1.0 O B:HOH962 2.4 23.6 1.0 O B:HIS98 2.4 15.9 1.0 O B:LYS96 2.4 18.1 1.0 O B:HOH907 2.6 16.2 1.0 C B:LYS96 3.4 17.6 1.0 C B:HIS98 3.6 16.3 1.0 OD1 B:ASP398 3.9 16.8 1.0 CA B:LYS96 3.9 17.8 1.0 N B:HIS98 4.2 15.3 1.0 O B:LEU95 4.3 15.4 1.0 N B:LEU97 4.4 16.1 1.0 C B:LEU97 4.5 18.0 1.0 CA B:GLU99 4.5 17.6 1.0 N B:GLU99 4.5 16.5 1.0 CA B:HIS98 4.5 14.6 1.0 CG B:LYS96 4.5 27.3 1.0 O B:GLY397 4.6 15.7 1.0 O B:HOH913 4.8 32.5 1.0 CA B:LEU97 4.8 17.3 1.0 CB B:LYS96 4.8 22.0 1.0 CA B:ASP398 4.8 14.9 1.0 O B:LEU97 4.9 18.1 1.0 O B:HOH942 5.0 14.2 1.0 N B:LYS96 5.0 16.8 1.0 CG B:ASP398 5.0 16.7 1.0

R.Shishiuchi, H.Kang, T.Tagami, Y.Ueda, W.Lang, A.Kimura, M.Okuyama. Discovery of Alpha-L-Glucosidase Raises the Possibility of Alpha-L-Glucosides in Nature. Acs Omega V. 7 47411 2022.
ISSN: ESSN 2470-1343
PubMed: 36570207
DOI: 10.1021/ACSOMEGA.2C06991