Sodium in PDB 7xsg: Crystal Structure of CLAGL29B

The structure of Crystal Structure of CLAGL29B, PDB code: 7xsg 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)	45.42 / 1.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.132, 123.405, 166.605, 90, 90, 90
R / Rfree (%)	17.2 / 18.8

The binding sites of Sodium atom in the Crystal Structure of CLAGL29B (pdb code 7xsg). 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, PDB code: 7xsg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of CLAGL29B


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:34.0 occ:1.00 O A:HIS98 2.4 16.9 1.0 O A:LYS96 2.4 18.5 1.0 O A:HOH842 2.5 23.1 1.0 O A:HOH1007 2.6 34.5 1.0 O A:HOH955 2.8 16.2 1.0 O A:HOH1011 3.2 56.5 1.0 C A:LYS96 3.3 17.8 1.0 C A:HIS98 3.6 15.4 1.0 CA A:LYS96 3.8 18.0 1.0 OD1 A:ASP398 4.2 14.8 1.0 N A:HIS98 4.2 14.5 1.0 O A:LEU95 4.3 13.9 1.0 N A:LEU97 4.4 16.0 1.0 CG A:LYS96 4.5 28.1 1.0 CA A:HIS98 4.5 14.5 1.0 C A:LEU97 4.6 17.2 1.0 N A:GLU99 4.6 16.7 1.0 CA A:GLU99 4.7 18.4 1.0 CB A:LYS96 4.7 22.4 1.0 CA A:LEU97 4.9 17.1 1.0 O A:GLY397 4.9 14.2 1.0 N A:LYS96 4.9 14.7 1.0 O A:HOH946 5.0 34.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of CLAGL29B


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:19.8 occ:1.00 O B:HOH1034 2.2 28.4 1.0 O B:HOH1030 2.4 16.3 1.0 O B:HOH1086 2.4 24.8 1.0 O B:HIS98 2.4 12.7 1.0 O B:LYS96 2.5 14.4 1.0 O B:HOH988 2.6 12.1 1.0 C B:LYS96 3.4 12.4 1.0 C B:HIS98 3.6 10.6 1.0 OD1 B:ASP398 3.9 10.6 1.0 CA B:LYS96 3.9 13.0 1.0 OE2 B:GLU99 4.2 51.2 1.0 N B:HIS98 4.3 10.4 1.0 O B:LEU95 4.3 9.6 1.0 CA B:HIS98 4.5 10.5 1.0 CG B:LYS96 4.5 21.4 1.0 N B:LEU97 4.5 11.0 1.0 O B:GLY397 4.5 10.7 1.0 C B:LEU97 4.6 12.6 1.0 CA B:GLU99 4.6 16.1 1.0 N B:GLU99 4.6 15.1 1.0 O B:HOH920 4.7 27.0 1.0 CB B:LYS96 4.8 16.0 1.0 CD B:GLU99 4.9 36.7 1.0 CA B:ASP398 4.9 9.5 1.0 CA B:LEU97 4.9 12.0 1.0 CB B:HIS98 5.0 9.7 1.0 CG B:ASP398 5.0 10.7 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