Sodium in PDB 4u6b: ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans

The structure of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans, PDB code: 4u6b was solved by E.Ficko-Blean, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	187.790, 223.520, 225.220, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.5

The structure of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Sodium atom in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans (pdb code 4u6b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans, PDB code: 4u6b:

Sodium binding site 1 out of 1 in the ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of ZG3597, A Family 117 Glycoside Hydrolase, Produced By the Marine Bacterium Zobellia Galactanivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:66.7 occ:1.00 O A:PRO292 2.8 50.5 1.0 N A:ASP287 3.1 44.1 1.0 N A:ASP288 3.1 45.8 1.0 N A:PRO292 3.4 52.7 1.0 C A:GLY291 3.5 51.8 1.0 CB A:ALA286 3.6 38.0 1.0 CD A:PRO292 3.6 50.3 1.0 O A:GLY291 3.7 49.1 1.0 CA A:ALA286 3.7 38.5 1.0 CB A:ASP288 3.7 52.3 1.0 C A:PRO292 3.8 48.0 1.0 O A:ASP288 3.8 45.2 1.0 C A:ALA286 3.9 41.8 1.0 CA A:ASP288 3.9 47.0 1.0 CA A:ASP287 4.0 46.8 1.0 C A:ASP287 4.0 47.3 1.0 CG A:PRO292 4.1 54.0 1.0 CA A:PRO292 4.1 48.0 1.0 CB A:ASP287 4.2 53.9 1.0 C A:ASP288 4.4 48.7 1.0 CA A:GLY291 4.4 44.4 1.0 O A:HOH763 4.5 57.2 1.0 OD2 A:ASP287 4.7 68.3 1.0 CG A:ASP287 4.7 59.7 1.0 CB A:PRO292 4.8 53.5 1.0 N A:GLY291 4.9 37.0 1.0

E.Ficko-Blean, D.Duffieux, E.Rebuffet, R.Larocque, A.Groisillier, G.Michel, M.Czjzek. Biochemical and Structural Investigation of Two Paralogous Glycoside Hydrolases From Zobellia Galactanivorans: Novel Insights Into the Evolution, Dimerization Plasticity and Catalytic Mechanism of the GH117 Family Acta Crystallogr.,Sect.D 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004714025024