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Sodium in PDB 3ahd: Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate

Enzymatic activity of Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate

All present enzymatic activity of Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate:
4.1.2.22;

Protein crystallography data

The structure of Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate, PDB code: 3ahd 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) 34.12 / 1.90
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 174.448, 174.448, 163.847, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.7

Other elements in 3ahd:

The structure of Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate (pdb code 3ahd). 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 Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate, PDB code: 3ahd:

Sodium binding site 1 out of 1 in 3ahd

Go back to Sodium Binding Sites List in 3ahd
Sodium binding site 1 out of 1 in the Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phosphoketolase From Bifidobacterium Breve Complexed with 2-Acetyl- Thiamine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na828

b:30.7
occ:0.50
 OD1 A:ASP727 1.9 38.6 1.0
NE2 A:HIS726 2.1 31.6 1.0
CG A:ASP727 2.7 38.8 1.0
CD2 A:HIS726 2.9 27.2 1.0
OD2 A:ASP727 3.0 50.5 1.0
CE1 A:HIS726 3.1 31.0 1.0
O A:HOH1589 3.2 42.1 1.0
O A:HOH1605 4.0 17.5 0.5
CG A:HIS726 4.1 28.9 1.0
CB A:ASP727 4.1 32.3 1.0
ND1 A:HIS726 4.1 31.7 1.0
CA A:ASP727 4.5 31.2 1.0
N A:ASP727 4.6 29.8 1.0
O A:TYR721 4.9 29.7 1.0
O A:HOH1563 5.0 31.4 1.0

Reference:

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
Page generated: Sun Aug 17 12:41:30 2025

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