Sodium in PDB 8q1f: D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate

The structure of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate, PDB code: 8q1f was solved by F.A.Cruz-Navarrete, N.J.Baxter, A.J.Flinders, A.Buzoianu, M.J.Cliff, P.J.Baker, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.83 / 1.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.023, 79.663, 79.848, 90, 97.61, 90
R / Rfree (%)	11.5 / 13.5

The structure of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium atom in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate (pdb code 8q1f). 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 D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate, PDB code: 8q1f:

Sodium binding site 1 out of 1 in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:21.7 occ:1.00 O A:HOH533 2.3 25.3 1.0 O A:THR129 2.3 11.2 1.0 O A:HOH572 2.3 28.6 1.0 O A:PHE132 2.4 12.2 1.0 O A:HOH591 2.5 26.7 1.0 O A:HOH575 2.7 34.2 1.0 C A:THR129 3.4 9.4 1.0 C A:PHE132 3.5 8.7 1.0 CG2 A:THR129 3.8 13.1 1.0 N A:PHE132 4.0 8.9 1.0 CA A:PHE132 4.1 8.8 1.0 CB A:PHE132 4.2 9.1 1.0 CA A:THR129 4.3 9.1 1.0 N A:GLY130 4.3 9.1 1.0 CA A:GLY130 4.4 9.8 1.0 C A:GLY130 4.5 10.2 1.0 CB A:THR129 4.6 9.6 1.0 N A:ASP133 4.6 8.8 1.0 O A:GLY130 4.7 13.4 1.0 N A:TYR131 5.0 8.4 1.0 CA A:ASP133 5.0 9.4 1.0

F.A.Cruz-Navarrete, N.J.Baxter, A.J.Flinders, A.Buzoianu, M.J.Cliff, P.J.Baker, J.P.Waltho. Peri Active Site Catalysis of Proline Isomerisation Is the Molecular Basis of Allomorphy in Beta-Phosphoglucomutase. Commun Biol V. 7 909 2024.
ISSN: ESSN 2399-3642
PubMed: 39068257
DOI: 10.1038/S42003-024-06577-9