Sodium in PDB 2vy0: The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus

All present enzymatic activity of The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus:
3.2.1.39;

The structure of The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus, PDB code: 2vy0 was solved by A.Ilari, A.Fiorillo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.363, 84.762, 69.232, 90.00, 104.97, 90.00
R / Rfree (%)	19.1 / 22.9

The structure of The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus (pdb code 2vy0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus, PDB code: 2vy0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1297 b:52.2 occ:1.00 O A:ILE49 4.3 19.1 1.0 O A:LEU48 4.5 19.5 1.0 O A:HOH2007 4.5 16.8 1.0 C A:ILE49 4.5 18.7 1.0 CD2 A:HIS51 4.9 19.4 1.0 O A:HOH2022 4.9 18.9 1.0 CA A:ILE49 4.9 18.9 1.0 CD2 A:LEU48 4.9 20.0 1.0 NE2 A:HIS51 5.0 19.4 1.0

Sodium binding site 2 out of 3 in the The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1299 b:44.6 occ:1.00 OE1 B:GLU138 3.0 19.0 1.0 O B:HOH2110 3.5 37.9 1.0 CD B:GLU138 3.8 17.7 1.0 OE2 B:GLU138 3.9 19.7 1.0 CG1 B:VAL218 4.2 16.8 1.0 OH B:TYR231 4.3 16.6 1.0 CE1 B:TYR231 4.3 15.7 1.0 O B:HOH2111 4.6 38.1 1.0 CZ B:TYR231 4.7 16.1 1.0 CD1 B:ILE41 4.8 23.6 1.0 CD1 B:ILE39 4.9 27.6 1.0 O B:HOH2081 5.0 29.5 1.0

Sodium binding site 3 out of 3 in the The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The X-Ray Structure of Endo-Beta-1,3-Glucanase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1300 b:36.4 occ:1.00 NZ B:LYS124 3.4 22.2 1.0 OH B:TYR74 3.4 37.4 1.0 CE B:LYS124 3.9 21.1 1.0 CG2 B:THR65 4.2 20.8 1.0 O B:HOH2016 4.2 45.0 1.0 O B:PHE66 4.5 23.1 1.0 OE2 B:GLU67 4.6 29.0 1.0 CZ B:TYR74 4.7 37.8 1.0 CG B:GLU67 4.8 26.3 1.0 CD B:GLU67 5.0 27.6 1.0

A.Ilari, A.Fiorillo, S.Angelaccio, R.Florio, R.Chiaraluce, J.Van Der Oost, V.Consalvi. Crystal Structure of A Family 16 Endoglucanase From the Hyperthermophile Pyrococcus Furiosus- Structural Basis of Substrate Recognition. Febs J. V. 276 1048 2009.
ISSN: ISSN 1742-464X
PubMed: 19154353
DOI: 10.1111/J.1742-4658.2008.06848.X