Sodium in PDB 3zpy: Crystal Structure of the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans

All present enzymatic activity of Crystal Structure of the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans:
4.2.2.11; 4.2.2.3;

The structure of Crystal Structure of the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans, PDB code: 3zpy was solved by F.Thomas, A.Jeudy, G.Michel, M.Czjzek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.66 / 1.43
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.860, 50.390, 55.520, 69.14, 90.02, 84.92
R / Rfree (%)	15.96 / 20.451

The binding sites of Sodium atom in the Crystal Structure of the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans (pdb code 3zpy). 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 the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans, PDB code: 3zpy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans


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 the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na450 b:8.9 occ:1.00 O A:ALA235 2.7 16.9 1.0 O A:THR233 2.7 14.1 1.0 O A:ILE238 2.8 11.8 1.0 O A:HOH2344 2.9 27.4 1.0 O A:HOH2053 3.4 29.9 1.0 N A:ILE238 3.7 16.6 1.0 C A:ALA235 3.8 16.0 1.0 O A:HOH2054 3.8 21.0 1.0 C A:ILE238 3.8 12.0 1.0 C A:THR233 3.8 12.2 1.0 O A:HOH2048 4.0 31.3 1.0 N A:GLY237 4.0 20.3 1.0 CA A:ILE238 4.2 13.0 1.0 C A:ASP234 4.3 14.6 1.0 N A:ALA235 4.4 13.8 1.0 CB A:ILE238 4.5 13.5 1.0 CA A:SER236 4.5 18.4 0.5 C A:SER236 4.5 20.0 1.0 CA A:SER236 4.5 19.2 0.5 O A:ASP234 4.5 24.6 1.0 N A:SER236 4.6 15.9 1.0 C A:GLY237 4.6 18.7 1.0 CA A:THR233 4.7 11.6 1.0 CA A:ALA235 4.7 14.3 1.0 CA A:ASP234 4.7 14.6 1.0 N A:ASP234 4.7 11.7 1.0 CA A:GLY237 4.8 19.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans


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 the Marine PL7 Alginate Lyase ALYA1 From Zobellia Galactanivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na450 b:21.9 occ:1.00 OG1 B:THR233 2.7 12.4 1.0 O B:HOH2049 2.7 26.1 1.0 OD1 B:ASP234 2.8 18.3 1.0 C B:THR233 3.2 12.8 1.0 O B:THR233 3.3 13.7 1.0 N B:ASP234 3.4 11.8 1.0 CB B:THR233 3.6 11.6 1.0 CA B:ASP234 3.8 14.3 1.0 CG B:ASP234 3.9 15.8 1.0 CA B:THR233 3.9 12.1 1.0 O B:HOH2047 4.0 26.0 1.0 O B:HOH2046 4.1 19.3 1.0 OD2 B:ASP231 4.1 18.2 1.0 OD1 B:ASP231 4.4 10.4 1.0 CG B:ASP231 4.4 11.6 1.0 CB B:ASP234 4.4 15.1 1.0 N B:THR233 4.7 10.5 1.0 O B:HOH2054 4.7 20.3 1.0 OD2 B:ASP234 4.9 17.2 1.0 CG2 B:THR233 4.9 11.0 1.0 O B:HOH2112 5.0 28.1 1.0

F.Thomas, L.C.E.Lundqvist, M.Jam, A.Jeudy, T.Barbeyron, C.Sandstrom, G.Michel, M.Czjzek. Comparative Characterization of Two Marine Alginate Lyases From Zobellia Galactanivorans Reveals Distinct Modes of Action and Exquisite Adaptation to Their Natural Substrate. J.Biol.Chem. V. 288 23021 2013.
ISSN: ISSN 0021-9258
PubMed: 23782694
DOI: 10.1074/JBC.M113.467217