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Fluorine 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:

Magnesium (Mg) 2 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6ydj

Go back to Fluorine Binding Sites List in 6ydj
Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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:F302

b:6.8
occ:1.00
 F1 A:MGF302 0.0 6.8 1.0
MG A:MGF302 1.9 6.7 1.0
MG A:MG303 2.0 6.6 1.0
O2 A:BG6301 2.6 7.3 1.0
O A:HOH510 2.7 7.8 1.0
O1 A:BG6301 2.8 6.7 1.0
O A:HOH441 2.9 7.4 1.0
OD2 A:ASP8 2.9 7.0 1.0
O A:ASP10 2.9 6.4 1.0
OD1 A:ASP8 3.0 6.9 1.0
F2 A:MGF302 3.1 6.9 1.0
CB A:ASP10 3.2 6.0 1.0
CG A:ASP8 3.3 6.7 1.0
F3 A:MGF302 3.4 9.3 1.0
C2 A:BG6301 3.4 7.1 1.0
C1 A:BG6301 3.5 6.8 1.0
N A:ASP10 3.6 6.2 1.0
CA A:ASP10 3.6 5.9 1.0
C A:ASP10 3.7 5.8 1.0
OD2 A:ASP10 3.8 7.0 1.0
CG A:ASP10 4.0 6.1 1.0
OD1 A:ASP170 4.0 7.1 1.0
O A:HOH520 4.2 9.0 1.0
N A:GLY46 4.4 7.7 1.0
CA A:GLY46 4.5 7.8 1.0
C A:LEU9 4.6 6.2 1.0
N A:LEU9 4.8 6.2 1.0
CB A:ASP8 4.8 6.7 1.0
O5 A:BG6301 4.8 7.0 1.0
C3 A:BG6301 4.8 7.4 1.0
CG A:ASP170 4.9 7.0 1.0
N A:GLY11 5.0 6.2 1.0

Fluorine binding site 2 out of 3 in 6ydj

Go back to Fluorine Binding Sites List in 6ydj
Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F 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:F302

b:6.9
occ:1.00
 F2 A:MGF302 0.0 6.9 1.0
MG A:MGF302 1.9 6.7 1.0
OG A:SER114 2.6 8.5 1.0
O1 A:BG6301 2.7 6.7 1.0
N A:ASP10 2.8 6.2 1.0
OD1 A:ASP8 2.8 6.9 1.0
N A:LEU9 2.9 6.2 1.0
F1 A:MGF302 3.1 6.8 1.0
CB A:SER114 3.2 8.3 1.0
CB A:LEU9 3.3 6.7 1.0
CA A:LEU9 3.3 6.4 1.0
OD2 A:ASP10 3.3 7.0 1.0
F3 A:MGF302 3.4 9.3 1.0
C A:LEU9 3.5 6.2 1.0
CG A:ASP10 3.6 6.1 1.0
CG A:ASP8 3.6 6.7 1.0
CA A:SER114 3.7 9.0 1.0
CB A:ASP10 3.8 6.0 1.0
CA A:ASP10 3.9 5.9 1.0
OD2 A:ASP8 4.1 7.0 1.0
C A:ASP8 4.1 6.5 1.0
C1 A:BG6301 4.1 6.8 1.0
OD1 A:ASP10 4.3 6.8 1.0
N A:ALA115 4.4 9.1 1.0
CA A:ASP8 4.4 6.6 1.0
C A:SER114 4.5 8.4 1.0
MG A:MG303 4.5 6.6 1.0
CG A:LEU9 4.6 7.3 1.0
CB A:ASP8 4.6 6.7 1.0
O A:ASP10 4.6 6.4 1.0
CB A:SER116 4.7 7.4 1.0
O A:LEU9 4.7 6.7 1.0
C A:ASP10 4.7 5.8 1.0
N A:SER116 4.7 8.1 1.0
O5 A:BG6301 4.8 7.0 1.0
N A:SER114 4.8 8.7 1.0
C2 A:BG6301 4.9 7.1 1.0
O2 A:BG6301 4.9 7.3 1.0
CD2 A:LEU9 5.0 8.0 1.0

Fluorine binding site 3 out of 3 in 6ydj

Go back to Fluorine Binding Sites List in 6ydj
Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F binding site number 3 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:F302

b:9.3
occ:1.00
 F3 A:MGF302 0.0 9.3 1.0
MG A:MGF302 1.9 6.7 1.0
NZ A:LYS145 2.6 7.7 1.0
O1 A:BG6301 2.8 6.7 1.0
N A:ALA115 2.8 9.1 1.0
OD1 A:ASP8 2.8 6.9 1.0
C1 A:BG6301 3.2 6.8 1.0
CB A:ALA115 3.3 10.8 1.0
F2 A:MGF302 3.4 6.9 1.0
F1 A:MGF302 3.4 6.8 1.0
CE A:LYS145 3.4 8.2 1.0
CA A:ALA115 3.6 9.6 1.0
C A:SER114 3.7 8.4 1.0
CA A:SER114 3.7 9.0 1.0
CD A:LYS145 3.8 8.9 1.0
O A:HOH510 3.9 7.8 1.0
CG A:ASP8 4.0 6.7 1.0
CA A:GLY46 4.1 7.8 1.0
OG A:SER114 4.1 8.5 1.0
O A:GLY46 4.1 9.1 1.0
O2 A:BG6301 4.2 7.3 1.0
O5 A:BG6301 4.2 7.0 1.0
C2 A:BG6301 4.3 7.1 1.0
O A:ALA113 4.3 9.3 1.0
CB A:SER114 4.5 8.3 1.0
C A:GLY46 4.5 7.8 1.0
OE2 A:GLU169 4.5 11.1 1.0
C A:ALA115 4.5 8.9 1.0
N A:SER116 4.5 8.1 1.0
OD2 A:ASP8 4.6 7.0 1.0
MG A:MG303 4.8 6.6 1.0
N A:SER114 4.8 8.7 1.0
O A:SER114 4.9 10.9 1.0
N A:GLY46 5.0 7.7 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: Tue Jul 15 17:41:26 2025

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