Sodium in PDB 3wz1: Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94

All present enzymatic activity of Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94:
3.2.1.81;

The structure of Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94, PDB code: 3wz1 was solved by E.Takagi, Y.Hatada, M.Akita, Y.Ohta, G.Yokoi, T.Miyazaki, A.Nishikawa, T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.86 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.624, 69.394, 90.367, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 16.5

The binding sites of Sodium atom in the Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94 (pdb code 3wz1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94, PDB code: 3wz1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:10.8 occ:1.00 OD2 A:ASP22 2.3 12.4 1.0 O A:ASP285 2.3 9.4 1.0 O A:GLY90 2.3 12.5 1.0 O A:ASP46 2.3 10.1 1.0 OD1 A:ASP285 2.4 10.6 1.0 C A:ASP285 3.3 9.2 1.0 CG A:ASP285 3.3 10.3 1.0 C A:ASP46 3.4 10.3 1.0 C A:GLY90 3.5 13.3 1.0 CG A:ASP22 3.5 12.1 1.0 O A:HOH660 3.6 27.8 1.0 CA A:ASP285 3.7 9.0 1.0 O A:HOH704 4.0 25.9 1.0 CA A:ASP46 4.0 10.1 1.0 CB A:ASP46 4.0 10.9 1.0 CB A:ASP285 4.1 9.6 1.0 OD1 A:ASN48 4.1 19.7 1.0 OD2 A:ASP285 4.2 11.6 1.0 CA A:GLY90 4.2 14.3 1.0 CB A:ASP22 4.2 11.3 1.0 ND2 A:ASN48 4.3 16.0 1.0 OD1 A:ASP22 4.4 13.1 1.0 N A:TRP286 4.5 9.1 1.0 N A:PHE47 4.5 10.0 1.0 CG A:ASN48 4.5 16.3 1.0 CB A:PHE47 4.5 10.1 1.0 N A:LYS91 4.5 12.6 1.0 NZ A:LYS91 4.6 20.9 1.0 C A:PHE47 4.6 11.3 1.0 CA A:PHE47 4.7 10.6 1.0 CA A:LYS91 4.7 12.4 1.0 O A:PHE47 4.8 11.8 1.0 O A:HOH608 4.8 24.5 1.0 CD A:LYS91 4.8 18.3 1.0 CG A:ASP46 4.9 11.9 1.0 CA A:TRP286 4.9 9.5 1.0 CB A:TRP286 5.0 10.8 1.0

Sodium binding site 2 out of 2 in the Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Catalytic Domain of Beta-Agarase From Microbulbifer Thermotolerans Jamb-A94 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:14.4 occ:1.00 OE2 A:GLU146 2.3 12.5 1.0 O A:GLY245 2.4 12.3 1.0 OG A:SER247 2.4 11.8 1.0 OG1 A:THR244 2.4 13.8 1.0 O A:HOH560 2.6 19.8 1.0 CD A:GLU146 3.0 12.0 1.0 OE1 A:GLU146 3.1 11.3 1.0 CB A:THR244 3.3 13.6 1.0 C A:GLY245 3.5 11.6 1.0 CB A:SER247 3.5 11.1 1.0 N A:SER247 3.6 11.0 1.0 C A:THR244 3.7 13.1 1.0 O A:THR244 3.8 12.7 1.0 N A:GLY245 3.9 12.0 1.0 O A:HOH707 4.0 30.5 1.0 CA A:SER247 4.1 11.3 1.0 CA A:THR244 4.1 13.5 1.0 O A:HOH537 4.1 15.0 1.0 CB A:THR241 4.2 13.2 1.0 N A:LYS248 4.2 10.9 1.0 CG A:LYS248 4.3 11.2 1.0 CA A:GLY245 4.3 12.0 1.0 CG A:GLU146 4.4 10.9 1.0 CE A:LYS248 4.4 12.1 1.0 CG2 A:THR244 4.4 14.3 1.0 N A:LEU246 4.5 10.4 1.0 C A:SER247 4.5 11.1 1.0 C A:LEU246 4.6 10.8 1.0 CG2 A:THR241 4.6 13.5 1.0 CA A:LEU246 4.6 10.8 1.0 O A:THR241 4.6 14.6 1.0 CD A:LYS248 4.7 11.5 1.0 OG1 A:THR241 4.8 12.5 1.0 N A:THR244 5.0 13.9 1.0

E.Takagi, Y.Hatada, M.Akita, Y.Ohta, G.Yokoi, T.Miyazaki, A.Nishikawa, T.Tonozuka. Crystal Structure of the Catalytic Domain of A GH16 Beta-Agarase From A Deep-Sea Bacterium, Microbulbifer Thermotolerans Jamb-A94 To Be Published.