Sodium in PDB 5dgq: Crystal Structure of GH9 Exo-Beta-D-Glucosaminidase PBPRA0520

The structure of Crystal Structure of GH9 Exo-Beta-D-Glucosaminidase PBPRA0520, PDB code: 5dgq was solved by K.Suzuki, Y.Honda, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.87 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.928, 102.318, 90.280, 90.00, 97.72, 90.00
R / Rfree (%)	15.7 / 20.6

The binding sites of Sodium atom in the Crystal Structure of GH9 Exo-Beta-D-Glucosaminidase PBPRA0520 (pdb code 5dgq). 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 GH9 Exo-Beta-D-Glucosaminidase PBPRA0520, PDB code: 5dgq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of GH9 Exo-Beta-D-Glucosaminidase PBPRA0520


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 GH9 Exo-Beta-D-Glucosaminidase PBPRA0520 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:12.3 occ:1.00 O A:GLN243 2.2 11.7 1.0 O A:HOH1070 2.3 16.0 1.0 O A:HOH941 2.4 15.9 1.0 O A:TYR301 2.4 14.9 1.0 OE1 A:GLN248 2.8 11.8 1.0 O A:ASP241 3.2 15.5 1.0 C A:GLN243 3.4 13.1 1.0 C A:TYR301 3.5 15.8 1.0 CD A:GLN248 3.6 12.8 1.0 CE A:MET213 3.6 14.2 1.0 NE2 A:GLN248 3.7 13.0 1.0 CB A:TYR301 3.8 14.2 1.0 CA A:TYR301 3.8 15.3 1.0 C A:ASP241 4.0 15.4 1.0 N A:GLN243 4.1 13.0 1.0 O A:HOH1091 4.1 20.0 1.0 CA A:GLN243 4.2 13.1 1.0 CB A:ASP241 4.4 21.6 1.0 N A:ALA244 4.4 11.0 1.0 O A:HOH989 4.4 22.2 1.0 N A:GLY245 4.5 12.3 1.0 CA A:ALA244 4.5 10.0 1.0 C A:TYR242 4.6 15.0 1.0 CB A:GLN243 4.6 14.9 1.0 CA A:ASP241 4.7 15.5 1.0 N A:LEU302 4.7 14.3 1.0 CG A:TYR301 4.7 16.3 1.0 OE1 A:GLN243 4.8 17.8 1.0 N A:TYR242 4.8 14.2 1.0 OD2 A:ASP303 4.8 14.6 1.0 C A:ALA244 4.9 10.9 1.0 CA A:TYR242 5.0 14.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of GH9 Exo-Beta-D-Glucosaminidase PBPRA0520


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 GH9 Exo-Beta-D-Glucosaminidase PBPRA0520 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:19.8 occ:1.00 O B:GLN243 2.3 14.5 1.0 O B:HOH996 2.3 17.8 1.0 O B:HOH988 2.5 17.4 1.0 O B:TYR301 2.5 19.7 1.0 OE1 B:GLN248 2.6 15.1 1.0 O B:ASP241 3.2 20.1 1.0 CD B:GLN248 3.5 15.3 1.0 C B:GLN243 3.5 14.5 1.0 C B:TYR301 3.5 20.4 1.0 CE B:MET213 3.6 19.1 1.0 NE2 B:GLN248 3.6 14.3 1.0 CA B:TYR301 3.9 20.2 1.0 CB B:TYR301 3.9 17.4 1.0 C B:ASP241 4.1 20.7 1.0 N B:GLN243 4.2 14.7 1.0 O B:HOH1037 4.2 25.6 1.0 CA B:GLN243 4.4 15.9 1.0 N B:ALA244 4.4 11.7 1.0 N B:GLY245 4.4 15.2 1.0 CA B:ALA244 4.5 12.9 1.0 O B:HOH823 4.6 25.3 1.0 CB B:ASP241 4.6 27.6 1.0 C B:TYR242 4.7 17.0 1.0 CB B:GLN243 4.7 19.0 1.0 N B:LEU302 4.8 18.6 1.0 OD2 B:ASP303 4.8 17.5 1.0 CG B:TYR301 4.8 18.6 1.0 OE1 B:GLN243 4.8 21.0 1.0 N B:TYR242 4.9 18.3 1.0 C B:ALA244 4.9 12.4 1.0 CA B:ASP241 4.9 22.5 1.0 CG B:GLN248 4.9 14.3 1.0

Y.Honda, S.Arai, K.Suzuki, M.Kitaoka, S.Fushinobu. The Crystal Structure of An Inverting Glycoside Hydrolase Family 9 Exo-Beta-D-Glucosaminidase and the Design of Glycosynthase. Biochem.J. V. 473 463 2016.
ISSN: ESSN 1470-8728
PubMed: 26621872
DOI: 10.1042/BJ20150966