Sodium in PDB 3akf: Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase

All present enzymatic activity of Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase:
3.2.1.55;

The structure of Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase, PDB code: 3akf was solved by Z.Fujimoto, H.Ichinose, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.81 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.961, 91.481, 135.451, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.4

The structure of Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase (pdb code 3akf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase, PDB code: 3akf:

Sodium binding site 1 out of 1 in the Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase


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-1,5-Alpha-L-Arabinofuranosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:26.4 occ:1.00 O A:HOH770 2.2 34.8 1.0 O A:HOH676 2.2 18.1 1.0 O A:HOH670 2.4 24.1 1.0 OE2 A:GLU79 2.5 26.8 1.0 O A:HOH771 2.5 22.9 1.0 CE1 A:HIS260 3.3 31.0 1.0 CD A:GLU79 3.5 23.3 1.0 CG A:GLU79 3.8 24.7 1.0 O A:HOH618 3.8 22.5 1.0 O A:PRO198 4.1 24.5 1.0 ND1 A:HIS260 4.1 29.8 1.0 NE2 A:HIS260 4.2 32.7 1.0 O A:HOH635 4.2 28.0 1.0 O A:ASP135 4.5 22.5 1.0 OE1 A:GLU79 4.6 24.5 1.0 O A:ASN261 4.7 29.7 1.0 CA A:GLY197 4.7 27.1 1.0 C A:GLY197 4.8 26.5 1.0 O A:ALA136 4.8 22.6 1.0 CB A:THR137 4.8 23.1 1.0 O A:GLY197 4.8 26.6 1.0 C A:ASP135 4.9 22.9 1.0 CA A:ASP135 4.9 23.4 1.0 CB A:ASP135 4.9 23.6 1.0 O A:ALA77 5.0 29.5 1.0 OD1 A:ASP135 5.0 24.8 1.0

Z.Fujimoto, H.Ichinose, T.Maehara, M.Honda, M.Kitaoka, S.Kaneko. Crystal Structure of An Exo-1,5-{Alpha}-L-Arabinofuranosidase From Streptomyces Avermitilis Provides Insights Into the Mechanism of Substrate Discrimination Between Exo- and Endo-Type Enzymes in Glycoside Hydrolase Family 43. J.Biol.Chem. V. 285 34134 2010.
ISSN: ISSN 0021-9258
PubMed: 20739278
DOI: 10.1074/JBC.M110.164251