Sodium in PDB 3ut0: Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1

The structure of Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1, PDB code: 3ut0 was solved by Y.Nakatani, S.M.Cutfield, J.F.Cutfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.33 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.908, 257.821, 85.605, 90.00, 115.47, 90.00
R / Rfree (%)	22.3 / 27

The structure of Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1 (pdb code 3ut0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1, PDB code: 3ut0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1


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 Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:18.4 occ:1.00 O A:ALA92 2.5 34.4 1.0 OD2 A:ASP98 2.5 51.9 1.0 O A:ILE100 2.5 33.0 1.0 O A:HOH838 2.5 36.6 1.0 O A:HOH833 2.5 29.9 1.0 OD1 A:ASP98 2.8 43.0 1.0 CG A:ASP98 3.0 56.9 1.0 O A:ASP94 3.2 60.8 1.0 C A:ALA92 3.5 47.1 1.0 C A:ILE100 3.6 34.7 1.0 C A:ASP94 3.8 46.7 1.0 CA A:ALA92 4.1 51.5 1.0 CG2 A:ILE100 4.3 26.0 1.0 CA A:ALA101 4.3 35.3 1.0 CA A:GLY58 4.3 48.7 1.0 N A:ASP94 4.4 28.6 1.0 CA A:SER95 4.4 37.5 1.0 N A:ALA101 4.4 44.8 1.0 O A:ALA91 4.4 34.5 1.0 N A:SER95 4.4 42.6 1.0 CB A:ASP98 4.5 54.7 1.0 N A:ILE102 4.5 47.7 1.0 C A:MET93 4.5 27.2 1.0 N A:ILE100 4.5 30.9 1.0 N A:MET93 4.6 40.2 1.0 CA A:ILE100 4.6 20.0 1.0 O A:MET93 4.7 50.7 1.0 O A:ILE102 4.7 28.4 1.0 CA A:ASP94 4.7 45.0 1.0 CA A:MET93 4.8 38.4 1.0 C A:ALA101 5.0 33.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1


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 Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:24.4 occ:1.00 O B:ILE100 2.5 33.5 1.0 OD2 B:ASP98 2.5 56.3 1.0 O B:ALA92 2.5 40.3 1.0 O B:HOH832 2.5 40.9 1.0 O B:HOH837 2.5 45.8 1.0 OD1 B:ASP98 2.7 52.1 1.0 CG B:ASP98 2.9 61.1 1.0 O B:ASP94 3.2 57.2 1.0 C B:ALA92 3.6 51.5 1.0 C B:ILE100 3.6 30.9 1.0 C B:ASP94 3.9 47.7 1.0 CA B:ALA92 4.2 48.5 1.0 CG2 B:ILE100 4.2 36.3 1.0 CA B:GLY58 4.3 39.0 1.0 CA B:ALA101 4.3 41.1 1.0 CB B:ASP98 4.4 50.7 1.0 CA B:SER95 4.4 26.3 1.0 N B:ALA101 4.4 46.0 1.0 N B:SER95 4.4 49.3 1.0 C B:MET93 4.4 36.4 1.0 N B:ASP94 4.5 48.2 1.0 O B:ALA91 4.5 42.1 1.0 N B:ILE100 4.5 27.9 1.0 O B:MET93 4.5 50.3 1.0 N B:ILE102 4.6 48.6 1.0 CA B:ILE100 4.6 20.7 1.0 N B:MET93 4.6 47.3 1.0 O B:ILE102 4.7 29.3 1.0 CA B:ASP94 4.8 56.0 1.0 CA B:MET93 4.9 36.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na902 b:24.5 occ:1.00 O C:ALA92 2.5 38.6 1.0 O C:HOH830 2.5 24.5 1.0 OD2 C:ASP98 2.5 57.1 1.0 O C:HOH833 2.5 49.0 1.0 O C:ILE100 2.5 25.1 1.0 OD1 C:ASP98 2.7 53.5 1.0 CG C:ASP98 3.0 59.7 1.0 O C:ASP94 3.2 67.2 1.0 C C:ALA92 3.5 40.2 1.0 C C:ILE100 3.6 35.5 1.0 C C:ASP94 3.9 48.2 1.0 CA C:ALA92 4.1 51.4 1.0 CG2 C:ILE100 4.2 27.7 1.0 CA C:GLY58 4.3 42.8 1.0 CA C:ALA101 4.3 49.3 1.0 C C:MET93 4.4 21.7 1.0 N C:ALA101 4.4 42.4 1.0 CB C:ASP98 4.4 51.7 1.0 CA C:SER95 4.4 23.5 1.0 O C:ALA91 4.4 38.6 1.0 N C:SER95 4.5 43.3 1.0 N C:ASP94 4.5 27.6 1.0 O C:MET93 4.5 57.2 1.0 N C:ILE102 4.5 54.0 1.0 N C:ILE100 4.6 29.6 1.0 CA C:ILE100 4.6 17.3 1.0 N C:MET93 4.6 51.6 1.0 O C:ILE102 4.7 32.2 1.0 CA C:ASP94 4.8 46.9 1.0 CA C:MET93 4.8 38.3 1.0 C C:ALA101 5.0 41.5 1.0 N C:GLY58 5.0 30.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Exo-1,3/1,4-Beta-Glucanase (Exop) From Pseudoalteromonas Sp. BB1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na902 b:27.8 occ:1.00 O D:ILE100 2.5 28.0 1.0 O D:HOH831 2.5 62.1 1.0 O D:HOH828 2.5 33.0 1.0 OD2 D:ASP98 2.5 62.0 1.0 O D:ALA92 2.5 51.3 1.0 OD1 D:ASP98 2.7 53.0 1.0 CG D:ASP98 2.9 65.4 1.0 O D:ASP94 3.2 64.0 1.0 C D:ALA92 3.6 47.6 1.0 C D:ILE100 3.6 44.9 1.0 C D:ASP94 3.9 49.9 1.0 CA D:ALA92 4.2 50.1 1.0 CA D:GLY58 4.3 50.1 1.0 CG2 D:ILE100 4.3 36.5 1.0 CA D:ALA101 4.4 42.8 1.0 CB D:ASP98 4.4 56.9 1.0 C D:MET93 4.4 32.2 1.0 N D:ALA101 4.4 54.5 1.0 CA D:SER95 4.5 30.0 1.0 O D:ALA91 4.5 41.0 1.0 N D:SER95 4.5 43.1 1.0 O D:MET93 4.5 51.7 1.0 N D:ILE100 4.6 33.5 1.0 N D:ASP94 4.6 31.3 1.0 N D:ILE102 4.6 42.7 1.0 CA D:ILE100 4.6 26.9 1.0 N D:MET93 4.6 47.2 1.0 O D:ILE102 4.7 31.7 1.0 O D:HOH847 4.8 29.4 1.0 CA D:ASP94 4.8 52.2 1.0 CA D:MET93 4.9 41.8 1.0 N D:GLY58 5.0 52.9 1.0

Y.Nakatani, S.M.Cutfield, N.P.Cowieson, J.F.Cutfield. Structure and Activity of Exo-1,3/1,4-Beta-Glucanase From Marine Bacterium Pseudoalteromonas Sp. BB1 Showing A Novel C-Terminal Domain Febs J. 2011.
ISSN: ISSN 1742-464X
PubMed: 22129429
DOI: 10.1111/J.1742-4658.2011.08439.X