Atomistry » Fluorine » PDB 6y8n-6yhb » 6ydj
Atomistry »
  Fluorine »
    PDB 6y8n-6yhb »
      6ydj »

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: Fri Aug 2 04:30:06 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy