Sodium in PDB 3ahh: H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate

All present enzymatic activity of H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate:
4.1.2.22;

The structure of H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate, PDB code: 3ahh 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)	34.15 / 2.10
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	174.606, 174.606, 163.644, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.6

The structure of H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate (pdb code 3ahh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate, PDB code: 3ahh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with 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 H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na828 b:21.6 occ:0.50 O A:HOH870 2.3 22.3 1.0 O A:VAL507 2.4 16.3 1.0 NE2 A:HIS480 2.5 14.8 1.0 O A:HOH867 3.1 19.5 1.0 CE1 A:HIS480 3.2 12.3 1.0 C A:VAL507 3.6 14.2 1.0 CD2 A:HIS480 3.6 15.6 1.0 CG1 A:VAL507 4.3 14.3 1.0 CA A:VAL507 4.4 14.1 1.0 ND1 A:HIS480 4.4 15.3 1.0 OG A:SER510 4.5 19.7 1.0 N A:ILE508 4.6 15.2 1.0 CA A:ILE508 4.6 15.3 1.0 CG A:HIS480 4.6 15.9 1.0

Sodium binding site 2 out of 2 in the H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of H142A Mutant of Phosphoketolase From Bifidobacterium Breve Complexed with Acetyl Thiamine Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1397 b:22.1 occ:0.50 OD1 A:ASP727 1.7 36.8 1.0 NE2 A:HIS726 2.0 26.7 1.0 CG A:ASP727 2.9 38.9 1.0 CD2 A:HIS726 3.0 26.8 1.0 CE1 A:HIS726 3.0 26.8 1.0 OD2 A:ASP727 3.4 53.5 1.0 O A:HOH1396 3.7 37.7 0.5 ND1 A:HIS726 4.1 29.2 1.0 CG A:HIS726 4.1 30.9 1.0 CB A:ASP727 4.2 31.8 1.0 CA A:ASP727 4.6 30.8 1.0 N A:ASP727 4.7 29.7 1.0 O A:TYR721 4.7 29.1 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