Sodium in PDB 5dgr: Crystal Structure of GH9 Exo-Beta-D-Glucosaminidase PBPRA0520, Glucosamine Complex

The structure of Crystal Structure of GH9 Exo-Beta-D-Glucosaminidase PBPRA0520, Glucosamine Complex, PDB code: 5dgr 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)	28.90 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.294, 102.590, 89.804, 90.00, 97.22, 90.00
R / Rfree (%)	16.2 / 20.4

The binding sites of Sodium atom in the Crystal Structure of GH9 Exo-Beta-D-Glucosaminidase PBPRA0520, Glucosamine Complex (pdb code 5dgr). 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, Glucosamine Complex, PDB code: 5dgr:
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, Glucosamine Complex


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, Glucosamine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:26.4 occ:1.00 O A:GLN243 2.4 17.5 1.0 O A:HOH1021 2.4 23.3 1.0 O A:TYR301 2.5 21.2 1.0 O A:HOH801 2.6 28.0 1.0 OE1 A:GLN248 2.7 17.3 1.0 O A:ASP241 3.2 25.6 1.0 CD A:GLN248 3.5 18.8 1.0 C A:TYR301 3.5 21.9 1.0 C A:GLN243 3.6 20.0 1.0 NE2 A:GLN248 3.6 19.8 1.0 CE A:MET213 3.6 26.6 1.0 CA A:TYR301 3.9 20.8 1.0 CB A:TYR301 3.9 19.1 1.0 C A:ASP241 4.1 25.9 1.0 O A:HOH1044 4.1 25.4 1.0 N A:GLN243 4.2 19.8 1.0 CA A:GLN243 4.4 19.6 1.0 N A:ALA244 4.6 19.8 1.0 O A:HOH858 4.6 34.8 1.0 N A:GLY245 4.6 17.4 1.0 CA A:ALA244 4.6 18.1 1.0 CB A:ASP241 4.6 29.5 1.0 C A:TYR242 4.7 19.7 1.0 N A:LEU302 4.8 20.1 1.0 OD2 A:ASP303 4.8 20.6 1.0 CA A:ASP241 4.8 25.9 1.0 N A:TYR242 4.8 22.6 1.0 CB A:GLN243 4.8 19.8 1.0 OE1 A:GLN243 4.9 24.8 1.0 CG A:TYR301 4.9 19.6 1.0 CG A:GLN248 4.9 16.7 1.0 C A:ALA244 5.0 17.7 1.0

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


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, Glucosamine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:26.6 occ:1.00 O B:HOH927 2.3 28.8 1.0 O B:GLN243 2.4 18.0 1.0 O B:TYR301 2.6 21.5 1.0 O B:HOH904 2.7 22.7 1.0 OE1 B:GLN248 2.7 14.2 1.0 O B:ASP241 3.2 24.2 1.0 CD B:GLN248 3.5 16.2 1.0 C B:TYR301 3.6 22.5 1.0 C B:GLN243 3.6 18.9 1.0 NE2 B:GLN248 3.6 14.7 1.0 CE B:MET213 3.7 22.7 1.0 CA B:TYR301 3.9 21.6 1.0 CB B:TYR301 3.9 19.9 1.0 O B:HOH1010 4.1 29.5 1.0 C B:ASP241 4.1 24.0 1.0 N B:GLN243 4.3 19.8 1.0 N B:GLY245 4.4 18.8 1.0 CA B:GLN243 4.5 20.2 1.0 O B:HOH813 4.5 35.8 1.0 CA B:ALA244 4.6 16.4 1.0 N B:ALA244 4.6 15.3 1.0 CB B:ASP241 4.7 28.2 1.0 C B:TYR242 4.7 20.4 1.0 CG B:TYR301 4.8 20.1 1.0 OD2 B:ASP303 4.8 23.3 1.0 N B:LEU302 4.8 18.4 1.0 CB B:GLN243 4.8 22.8 1.0 N B:TYR242 4.9 22.0 1.0 CA B:ASP241 4.9 24.2 1.0 OE1 B:GLN243 4.9 22.2 1.0 C B:ALA244 4.9 14.5 1.0 CG B:GLN248 4.9 14.2 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