Magnesium in PDB 8q1c: Substrate-Free D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis

The structure of Substrate-Free D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis, PDB code: 8q1c 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)	52.70 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.65, 117.251, 53.25, 90, 98.64, 90
R / Rfree (%)	21.1 / 27

The binding sites of Magnesium atom in the Substrate-Free D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis (pdb code 8q1c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Substrate-Free D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis, PDB code: 8q1c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Substrate-Free D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Substrate-Free D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:32.5 occ:1.00 OD2 A:ASP8 2.0 49.9 1.0 OD1 A:ASP170 2.1 32.6 1.0 O A:HOH463 2.2 34.3 1.0 O A:HOH440 2.2 39.5 1.0 O A:ASN10 2.3 32.3 1.0 O A:HOH454 2.4 37.3 1.0 CG A:ASP170 3.2 35.5 1.0 CG A:ASP8 3.2 46.3 1.0 C A:ASN10 3.4 22.8 1.0 OE1 A:GLU169 3.5 40.5 1.0 OD2 A:ASP170 3.6 32.3 1.0 OD1 A:ASP8 3.8 32.6 1.0 CD A:GLU169 4.3 34.4 1.0 N A:ASP170 4.3 29.1 1.0 CA A:ASN10 4.3 27.9 1.0 ND2 A:ASN10 4.3 25.6 1.0 CB A:ASP8 4.3 30.0 1.0 CB A:ASN10 4.3 20.7 1.0 OE2 A:GLU169 4.4 40.0 1.0 O A:HOH504 4.4 40.8 1.0 CB A:ASP170 4.4 28.1 1.0 N A:GLY11 4.4 26.8 1.0 N A:ASN10 4.4 22.2 1.0 CA A:GLY11 4.5 23.5 1.0 CA A:ASP170 4.8 27.4 1.0 N A:SER171 4.8 26.9 1.0 CG A:ASN10 4.8 23.9 1.0 OG A:SER171 4.8 38.2 1.0 CB A:SER171 4.9 35.8 1.0 CG2 A:VAL12 4.9 28.1 1.0 C A:ASP170 4.9 30.6 1.0 C A:GLY11 5.0 21.9 1.0

Magnesium binding site 2 out of 2 in the Substrate-Free D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Substrate-Free D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:38.2 occ:1.00 O B:HOH456 2.1 41.4 1.0 O B:ASN10 2.2 30.7 1.0 OD1 B:ASP170 2.2 32.2 1.0 OD2 B:ASP8 2.3 46.0 1.0 OE1 B:GLU169 2.9 34.6 1.0 CG B:ASP170 3.2 34.8 1.0 C B:ASN10 3.3 23.1 1.0 CG B:ASP8 3.5 46.6 1.0 O B:HOH426 3.8 37.6 1.0 CD B:GLU169 3.8 46.9 1.0 OD2 B:ASP170 3.8 40.8 1.0 CB B:ASP8 4.1 41.5 1.0 OE2 B:GLU169 4.1 42.4 1.0 N B:ASP170 4.1 36.6 1.0 CA B:ASN10 4.2 26.9 1.0 N B:GLY11 4.3 33.6 1.0 CB B:ASP170 4.3 26.8 1.0 CB B:ASN10 4.4 29.4 1.0 ND2 B:ASN10 4.4 34.3 1.0 N B:ASN10 4.4 27.2 1.0 CA B:GLY11 4.4 29.6 1.0 OD1 B:ASP8 4.5 38.0 1.0 CA B:ASP170 4.7 30.9 1.0 CG2 B:VAL12 4.7 33.4 1.0 N B:SER171 4.7 30.5 1.0 CB B:SER171 4.8 41.4 1.0 OG B:SER171 4.9 38.9 1.0 CG B:ASN10 4.9 24.9 1.0 C B:ASP170 4.9 39.7 1.0 C B:GLY11 4.9 43.5 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