Sodium in PDB 7xsf: Crystal Structure of CLAGL29A

The structure of Crystal Structure of CLAGL29A, PDB code: 7xsf 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)	47.81 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.577, 95.521, 83.55, 90, 97.33, 90
R / Rfree (%)	20.5 / 24.3

The binding sites of Sodium atom in the Crystal Structure of CLAGL29A (pdb code 7xsf). 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 CLAGL29A, PDB code: 7xsf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of CLAGL29A


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 CLAGL29A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:46.7 occ:1.00 O A:HOH818 2.2 39.3 1.0 O A:HOH779 2.3 40.5 1.0 O A:HOH791 2.4 40.9 1.0 O A:HIS87 2.4 40.8 1.0 O A:ASP85 2.4 44.5 1.0 O A:HOH771 2.7 37.4 1.0 C A:ASP85 3.2 46.1 1.0 C A:HIS87 3.6 39.0 1.0 CA A:ASP85 3.7 43.8 1.0 OD1 A:ASP386 3.9 39.7 1.0 O A:HOH770 4.1 36.4 1.0 N A:HIS87 4.3 40.4 1.0 N A:GLU86 4.3 45.7 1.0 O A:HOH708 4.3 41.2 1.0 O A:LEU84 4.4 40.0 1.0 CB A:ASP85 4.5 43.1 1.0 C A:GLU86 4.5 42.0 1.0 CA A:HIS87 4.5 37.4 1.0 N A:GLU88 4.6 39.3 1.0 OE1 A:GLU88 4.6 62.8 1.0 CA A:GLU88 4.6 42.8 1.0 O A:HOH719 4.7 44.8 1.0 CA A:GLU86 4.7 43.6 1.0 CD A:GLU88 4.8 57.8 1.0 O A:HOH760 4.9 36.7 1.0 N A:ASP85 4.9 40.8 1.0 O A:GLY385 4.9 37.3 1.0 OE2 A:GLU88 4.9 62.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of CLAGL29A


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 CLAGL29A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:57.7 occ:1.00 O B:HOH774 2.1 45.9 1.0 O B:HOH703 2.3 34.0 1.0 O B:HIS87 2.4 57.9 1.0 O B:ASP85 2.4 58.9 1.0 O B:HOH750 2.8 47.0 1.0 C B:ASP85 3.2 57.2 1.0 C B:HIS87 3.6 56.0 1.0 CA B:ASP85 3.7 53.4 1.0 OD1 B:ASP386 3.8 45.9 1.0 N B:HIS87 4.3 55.0 1.0 N B:GLU86 4.3 60.2 1.0 O B:LEU84 4.3 55.5 1.0 CB B:ASP85 4.5 50.4 1.0 CA B:HIS87 4.5 53.4 1.0 C B:GLU86 4.5 57.6 1.0 N B:GLU88 4.6 55.2 1.0 CA B:GLU88 4.6 54.5 1.0 OE1 B:GLU88 4.7 70.3 1.0 CA B:GLU86 4.8 59.5 1.0 O B:GLY385 4.8 40.3 1.0 O B:HOH764 4.8 39.7 1.0 N B:ASP85 4.9 52.9 1.0 CD B:GLU88 5.0 63.1 1.0 CG B:ASP386 5.0 44.2 1.0 CA B:ASP386 5.0 44.7 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