Sodium in PDB 2v5c: Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure

All present enzymatic activity of Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure:
3.2.1.52;

The structure of Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure, PDB code: 2v5c was solved by E.Ficko-Blean, K.J.Gregg, J.J.Adams, J.H.Hehemann, S.J.Smith, M.Czjzek, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	105.41 / 2.10
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	130.385, 150.046, 155.428, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.5

The structure of Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure also contains other interesting chemical elements:

Arsenic	(As)	5 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure (pdb code 2v5c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure, PDB code: 2v5c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1630 b:10.4 occ:1.00 OH A:TYR583 2.6 23.2 1.0 O A:PHE619 2.6 22.4 1.0 O A:ALA616 2.7 19.1 1.0 O A:HOH2571 2.9 25.4 1.0 O A:LEU617 3.0 21.4 1.0 SD A:MET571 3.6 20.1 1.0 CZ A:TYR583 3.6 23.4 1.0 C A:LEU617 3.6 20.4 1.0 CE1 A:TYR583 3.6 21.5 1.0 C A:ALA616 3.8 18.5 1.0 C A:PHE619 3.8 22.8 1.0 CA A:LEU617 3.9 19.5 1.0 N A:PHE619 4.2 22.1 1.0 CE A:MET571 4.3 17.6 1.0 N A:LEU617 4.3 19.0 1.0 C2 A:CAC1629 4.3 47.0 1.0 CA A:PHE619 4.5 22.7 1.0 OE1 A:GLN575 4.5 28.5 1.0 N A:SER618 4.5 20.8 1.0 CB A:MET571 4.6 20.1 1.0 O2 A:CAC1629 4.6 47.8 1.0 CG A:MET571 4.7 19.3 1.0 C A:SER618 4.8 21.6 1.0 CB A:PHE619 4.8 23.4 1.0 N A:ASP620 4.8 22.9 1.0 AS A:CAC1629 4.9 48.3 1.0 CD1 A:TYR583 4.9 22.3 1.0 CE2 A:TYR583 4.9 22.4 1.0 C1 A:CAC1629 4.9 48.4 1.0 CD A:GLN575 5.0 28.8 1.0 CA A:ALA616 5.0 18.5 1.0

Sodium binding site 2 out of 2 in the Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Family 84 Glycoside Hydrolase From Clostridium Perfringens, 2.1 Angstrom Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1629 b:33.6 occ:1.00 O B:PHE619 2.4 24.7 1.0 O B:ALA616 2.5 19.2 1.0 OH B:TYR583 2.7 27.5 1.0 O B:LEU617 3.2 19.8 1.0 OE1 B:GLN575 3.5 32.7 1.0 C B:PHE619 3.5 24.9 1.0 CE B:MET571 3.6 26.4 1.0 CZ B:TYR583 3.7 26.6 1.0 CE1 B:TYR583 3.7 24.6 1.0 C B:ALA616 3.7 19.1 1.0 C B:LEU617 3.7 19.4 1.0 N B:PHE619 3.9 23.6 1.0 CA B:LEU617 3.9 19.1 1.0 O B:HOH2556 4.0 31.5 1.0 CA B:PHE619 4.2 24.1 1.0 N B:LEU617 4.3 18.8 1.0 SD B:MET571 4.3 24.0 1.0 CD B:GLN575 4.5 32.3 1.0 CB B:PHE619 4.5 24.1 1.0 N B:SER618 4.6 20.1 1.0 N B:ASP620 4.6 26.2 1.0 C B:SER618 4.7 22.1 1.0 O B:HOH2191 4.9 33.9 1.0 CA B:ALA616 4.9 18.8 1.0 CA B:ASP620 4.9 27.6 1.0 NE2 B:GLN575 5.0 33.4 1.0 O B:HOH2513 5.0 43.0 1.0 CE2 B:TYR583 5.0 24.4 1.0 CB B:MET571 5.0 20.2 1.0 CD1 B:TYR583 5.0 25.3 1.0

E.Ficko-Blean, K.J.Gregg, J.J.Adams, J.H.Hehemann, S.J.Smith, M.Czjzek, A.B.Boraston. Portrait of An Enzyme: A Complete Structural Analysis of A Multi-Modular Beta-N- Acetylglucosaminidase From Clostridium Perfringens J.Biol.Chem. V. 284 9876 2009.
ISSN: ISSN 0021-9258
PubMed: 19193644
DOI: 10.1074/JBC.M808954200