Sodium in PDB 3ahc: Resting Form of Phosphoketolase From Bifidobacterium Breve

All present enzymatic activity of Resting Form of Phosphoketolase From Bifidobacterium Breve:
4.1.2.22;

The structure of Resting Form of Phosphoketolase From Bifidobacterium Breve, PDB code: 3ahc was solved by R.Suzuki, T.Katayama, B.-J.Kim, T.Wakagi, H.Shoun, H.Ashida, K.Yamamoto, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.18 / 1.70
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	174.766, 174.766, 163.839, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.1

The structure of Resting Form of Phosphoketolase From Bifidobacterium Breve also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Resting Form of Phosphoketolase From Bifidobacterium Breve (pdb code 3ahc). 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 Resting Form of Phosphoketolase From Bifidobacterium Breve, PDB code: 3ahc:

Sodium binding site 1 out of 1 in the Resting Form of Phosphoketolase From Bifidobacterium Breve


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Resting Form of Phosphoketolase From Bifidobacterium Breve within 5.0Å range: probe atom residue distance (Å) B Occ A:Na828 b:32.6 occ:0.50 NE2 A:HIS726 2.2 22.5 1.0 OD1 A:ASP727 2.2 28.9 1.0 CD2 A:HIS726 2.9 21.0 1.0 CG A:ASP727 3.2 32.8 1.0 O A:HOH1615 3.3 34.0 1.0 CE1 A:HIS726 3.3 22.5 1.0 OD2 A:ASP727 3.5 40.5 1.0 O A:HOH845 3.9 15.3 0.5 CG A:HIS726 4.1 22.9 1.0 ND1 A:HIS726 4.3 22.6 1.0 CB A:ASP727 4.5 25.1 1.0 N A:ASP727 4.8 21.2 1.0 O A:TYR721 4.8 23.0 1.0 CA A:ASP727 4.9 24.8 1.0 O A:HOH1591 4.9 24.1 1.0

R.Suzuki, T.Katayama, B.-J.Kim, T.Wakagi, H.Shoun, H.Ashida, K.Yamamoto, S.Fushinobu. Crystal Structures of Phosphoketolase: Thiamine Diphosphate-Dependent Dehydration Mechanism J.Biol.Chem. V. 285 34279 2010.
ISSN: ISSN 0021-9258
PubMed: 20739284
DOI: 10.1074/JBC.M110.156281