Magnesium in PDB 6ydm: Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound

All present enzymatic activity of Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound:
5.4.2.6;

The structure of Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound, PDB code: 6ydm was solved by H.P.Wood, F.A.Cruz-Navarrete, N.J.Baxter, C.R.Trevitt, A.J.Robertson, S.R.Dix, A.M.Hounslow, M.J.Cliff, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.61 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.130, 76.640, 117.260, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 29

The binding sites of Magnesium atom in the Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound (pdb code 6ydm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound, PDB code: 6ydm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:23.2 occ:1.00 OD1 A:ASP170 2.1 21.1 1.0 O A:HOH476 2.1 30.2 1.0 OD2 A:ASP8 2.3 22.0 1.0 O A:ASP10 2.3 22.3 1.0 OE1 A:GLU169 2.5 28.4 1.0 H A:ASP170 3.1 24.9 1.0 CG A:ASP170 3.3 24.1 1.0 O A:HOH416 3.4 27.9 1.0 CG A:ASP8 3.4 23.4 1.0 HB3 A:ASP8 3.4 24.5 1.0 C A:ASP10 3.5 23.9 1.0 CD A:GLU169 3.5 28.0 1.0 HG23 A:VAL12 3.6 24.5 1.0 HA3 A:GLY11 3.8 26.2 1.0 O A:HOH481 3.9 49.1 1.0 CB A:ASP8 3.9 24.8 1.0 OE2 A:GLU169 3.9 27.5 1.0 HB3 A:SER171 4.0 28.4 1.0 O A:HOH432 4.0 25.2 1.0 OD2 A:ASP170 4.0 24.4 1.0 N A:ASP170 4.0 25.2 1.0 HB3 A:ASP10 4.0 25.9 1.0 HA A:GLU169 4.1 23.6 1.0 H A:SER171 4.2 25.8 1.0 HB2 A:ASP8 4.3 24.5 1.0 CB A:ASP170 4.4 25.6 1.0 N A:GLY11 4.4 24.2 1.0 CA A:GLY11 4.5 26.0 1.0 OD1 A:ASP8 4.5 19.6 1.0 CA A:ASP10 4.5 25.9 1.0 N A:SER171 4.5 25.7 1.0 HB3 A:ASP170 4.5 25.0 1.0 CG2 A:VAL12 4.5 25.0 1.0 HG A:SER171 4.6 30.0 0.0 H A:ASP10 4.6 25.5 1.0 CA A:ASP170 4.6 26.1 1.0 OG A:SER171 4.6 28.3 1.0 N A:ASP10 4.6 26.8 1.0 O A:HOH471 4.6 32.3 1.0 CB A:ASP10 4.7 25.8 1.0 HG22 A:VAL12 4.7 24.2 1.0 CB A:SER171 4.7 28.7 1.0 H A:VAL12 4.8 23.5 1.0 C A:GLY11 4.8 26.5 1.0 HZ3 A:LYS145 4.8 27.3 1.0 CG A:GLU169 4.8 24.9 1.0 CA A:GLU169 4.9 24.1 1.0 C A:ASP170 4.9 26.0 1.0 N A:VAL12 4.9 23.7 1.0 C A:GLU169 4.9 26.1 1.0

Magnesium binding site 2 out of 2 in the Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-Phosphoglucomutase From Lactococcus Lactis with Citrate, Tris and Acetate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:29.8 occ:1.00 OD2 B:ASP8 2.1 30.2 1.0 OD1 B:ASP170 2.2 24.1 1.0 O B:HOH477 2.3 44.9 1.0 O B:ASP10 2.3 23.6 1.0 OE1 B:GLU169 2.4 26.8 1.0 H B:ASP170 3.1 26.5 1.0 CG B:ASP8 3.2 26.1 1.0 HB3 B:ASP8 3.2 27.0 1.0 CG B:ASP170 3.4 27.6 1.0 CD B:GLU169 3.5 28.6 1.0 HG23 B:VAL12 3.5 28.6 1.0 C B:ASP10 3.5 23.8 1.0 CB B:ASP8 3.7 27.0 1.0 O B:HOH425 3.8 35.0 1.0 OE2 B:GLU169 3.9 28.7 1.0 HA3 B:GLY11 3.9 27.6 1.0 HA B:GLU169 3.9 25.3 1.0 N B:ASP170 3.9 27.8 1.0 O B:HOH438 4.0 26.2 1.0 O B:HOH464 4.0 36.4 1.0 HB3 B:ASP10 4.0 24.4 1.0 HB3 B:SER171 4.1 28.3 1.0 OD2 B:ASP170 4.1 32.2 1.0 HB2 B:ASP8 4.1 26.7 1.0 H B:SER171 4.2 27.0 1.0 OD1 B:ASP8 4.3 21.4 1.0 CB B:ASP170 4.4 27.5 1.0 CG2 B:VAL12 4.4 29.3 1.0 N B:GLY11 4.4 24.2 1.0 CA B:ASP10 4.5 24.1 1.0 CA B:GLY11 4.5 28.1 1.0 HB3 B:ASP170 4.5 27.3 1.0 HG22 B:VAL12 4.5 28.2 1.0 N B:SER171 4.6 27.2 1.0 H B:ASP10 4.6 22.5 1.0 N B:ASP10 4.6 22.9 1.0 CA B:ASP170 4.6 27.2 1.0 HG B:SER171 4.7 30.0 0.0 HZ3 B:LYS145 4.7 27.4 1.0 OG B:SER171 4.7 32.1 1.0 CG B:GLU169 4.7 26.9 1.0 CA B:GLU169 4.7 25.8 1.0 CB B:ASP10 4.7 24.2 1.0 H B:VAL12 4.7 27.0 1.0 O B:HOH465 4.8 27.2 1.0 CB B:SER171 4.8 27.1 1.0 C B:GLY11 4.8 28.9 1.0 C B:GLU169 4.8 26.5 1.0 N B:VAL12 4.9 28.2 1.0 HG21 B:VAL12 4.9 29.2 1.0 C B:ASP170 4.9 27.9 1.0 HG2 B:GLU169 4.9 26.3 1.0 HZ1 B:LYS145 5.0 27.2 1.0

H.P.Wood, F.A.Cruz-Navarrete, N.J.Baxter, C.R.Trevitt, A.J.Robertson, S.R.Dix, A.M.Hounslow, M.J.Cliff, J.P.Waltho. Allomorphy As A Mechanism of Post-Translational Control of Enzyme Activity. Nat Commun V. 11 5538 2020.
ISSN: ESSN 2041-1723
PubMed: 33139716
DOI: 10.1038/S41467-020-19215-9