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Magnesium in PDB 6ydj: P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate

Enzymatic activity of P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate

All present enzymatic activity of P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate:
5.4.2.6;

Protein crystallography data

The structure of P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate, PDB code: 6ydj 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) 52.21 / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.080, 54.250, 104.320, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 16.9

Other elements in 6ydj:

The structure of P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate (pdb code 6ydj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate, PDB code: 6ydj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ydj

Go back to Magnesium Binding Sites List in 6ydj
Magnesium binding site 1 out of 2 in the P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:6.7
occ:1.00
 MG A:MGF302 0.0 6.7 1.0
F3 A:MGF302 1.9 9.3 1.0
F2 A:MGF302 1.9 6.9 1.0
F1 A:MGF302 1.9 6.8 1.0
OD1 A:ASP8 2.0 6.9 1.0
O1 A:BG6301 2.1 6.7 1.0
CG A:ASP8 3.0 6.7 1.0
C1 A:BG6301 3.2 6.8 1.0
OD2 A:ASP8 3.4 7.0 1.0
MG A:MG303 3.5 6.6 1.0
O A:HOH510 3.6 7.8 1.0
O2 A:BG6301 3.6 7.3 1.0
OG A:SER114 3.7 8.5 1.0
NZ A:LYS145 3.8 7.7 1.0
N A:ASP10 3.9 6.2 1.0
OD2 A:ASP10 3.9 7.0 1.0
C2 A:BG6301 3.9 7.1 1.0
N A:ALA115 4.0 9.1 1.0
N A:LEU9 4.0 6.2 1.0
CA A:SER114 4.1 9.0 1.0
CB A:ASP10 4.2 6.0 1.0
O5 A:BG6301 4.3 7.0 1.0
CB A:SER114 4.3 8.3 1.0
CG A:ASP10 4.4 6.1 1.0
CB A:ASP8 4.4 6.7 1.0
O A:ASP10 4.4 6.4 1.0
CA A:ASP10 4.5 5.9 1.0
C A:SER114 4.6 8.4 1.0
C A:LEU9 4.7 6.2 1.0
CA A:ASP8 4.7 6.6 1.0
O A:HOH441 4.8 7.4 1.0
CA A:GLY46 4.8 7.8 1.0
CA A:LEU9 4.8 6.4 1.0
OE2 A:GLU169 4.9 11.1 1.0
C A:ASP8 4.9 6.5 1.0
CB A:ALA115 4.9 10.8 1.0
CA A:ALA115 4.9 9.6 1.0
N A:SER116 5.0 8.1 1.0
C A:ASP10 5.0 5.8 1.0
CE A:LYS145 5.0 8.2 1.0

Magnesium binding site 2 out of 2 in 6ydj

Go back to Magnesium Binding Sites List in 6ydj
Magnesium binding site 2 out of 2 in the P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:6.6
occ:1.00
 F1 A:MGF302 2.0 6.8 1.0
OD2 A:ASP8 2.0 7.0 1.0
OD1 A:ASP170 2.1 7.1 1.0
O A:HOH441 2.1 7.4 1.0
O A:ASP10 2.1 6.4 1.0
O A:HOH510 2.1 7.8 1.0
CG A:ASP170 3.0 7.0 1.0
CG A:ASP8 3.1 6.7 1.0
C A:ASP10 3.3 5.8 1.0
OD2 A:ASP170 3.4 7.3 1.0
OD1 A:ASP8 3.4 6.9 1.0
MG A:MGF302 3.5 6.7 1.0
O2 A:BG6301 3.9 7.3 1.0
CA A:ASP10 4.0 5.9 1.0
OE1 A:GLU169 4.1 10.4 1.0
CB A:ASP10 4.1 6.0 1.0
N A:ASP10 4.1 6.2 1.0
N A:GLY11 4.3 6.2 1.0
CB A:ASP170 4.3 7.2 1.0
CB A:ASP8 4.4 6.7 1.0
F2 A:MGF302 4.5 6.9 1.0
O A:HOH520 4.5 9.0 1.0
CA A:GLY11 4.6 6.8 1.0
N A:ASP170 4.6 6.9 1.0
CD A:GLU169 4.7 8.2 1.0
OE2 A:GLU169 4.7 11.1 1.0
CB A:SER171 4.7 8.7 1.0
F3 A:MGF302 4.8 9.3 1.0
N A:GLY46 4.8 7.7 1.0
O1 A:BG6301 4.8 6.7 1.0
OG A:SER171 4.8 8.8 1.0
C A:LEU9 4.8 6.2 1.0
CG2 A:VAL12 4.9 7.8 1.0
CA A:ASP170 4.9 7.1 1.0
C A:GLY11 5.0 6.8 1.0

Reference:

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
Page generated: Wed Oct 2 00:18:08 2024

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