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Fluorine in PDB 6hdl: R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A.

Enzymatic activity of R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A.

All present enzymatic activity of R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A.:
5.4.2.6;

Protein crystallography data

The structure of R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A., PDB code: 6hdl was solved by H.P.Wood, A.J.Robertson, C.Bisson, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.35 / 1.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.550, 54.300, 104.200, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 16.4

Other elements in 6hdl:

The structure of R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A. 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 R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A. (pdb code 6hdl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A., PDB code: 6hdl:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6hdl

Go back to Fluorine Binding Sites List in 6hdl
Fluorine binding site 1 out of 3 in the R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:10.3
occ:1.00
F1 A:MGF303 0.0 10.3 1.0
MG A:MGF303 1.9 12.1 1.0
MG A:MG302 1.9 9.3 1.0
O2 A:BG6301 2.7 10.8 1.0
O A:HOH478 2.7 10.6 1.0
O1 A:BG6301 2.8 11.2 1.0
OD2 A:ASP8 2.9 9.4 1.0
OD1 A:ASP8 2.9 9.7 1.0
O A:ASP10 2.9 9.5 1.0
O A:HOH467 2.9 9.7 1.0
F2 A:MGF303 3.0 10.5 1.0
F3 A:MGF303 3.2 13.4 1.0
CB A:ASP10 3.2 8.8 1.0
CG A:ASP8 3.2 9.2 1.0
N A:ASP10 3.5 8.8 1.0
C2 A:BG6301 3.5 10.4 1.0
C1 A:BG6301 3.5 10.8 1.0
CA A:ASP10 3.6 8.4 1.0
C A:ASP10 3.7 8.7 1.0
OD2 A:ASP10 3.9 10.4 1.0
CG A:ASP10 4.0 8.9 1.0
OD1 A:ASP170 4.0 9.6 1.0
O A:HOH526 4.3 11.3 1.0
N A:GLY46 4.4 10.3 1.0
CA A:GLY46 4.4 10.4 1.0
C A:LEU9 4.5 7.9 1.0
N A:LEU9 4.7 8.4 1.0
CB A:ASP8 4.8 10.1 1.0
O5 A:BG6301 4.8 10.8 1.0
C3 A:BG6301 4.9 10.6 1.0
CG A:ASP170 4.9 10.0 1.0
N A:GLY11 4.9 8.4 1.0

Fluorine binding site 2 out of 3 in 6hdl

Go back to Fluorine Binding Sites List in 6hdl
Fluorine binding site 2 out of 3 in the R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:10.5
occ:1.00
F2 A:MGF303 0.0 10.5 1.0
MG A:MGF303 1.8 12.1 1.0
OG A:SER114 2.6 10.6 1.0
O1 A:BG6301 2.7 11.2 1.0
OD1 A:ASP8 2.7 9.7 1.0
N A:ASP10 2.8 8.8 1.0
N A:LEU9 2.9 8.4 1.0
F1 A:MGF303 3.0 10.3 1.0
CB A:SER114 3.2 10.9 1.0
F3 A:MGF303 3.2 13.4 1.0
CB A:LEU9 3.3 9.5 1.0
CA A:LEU9 3.3 8.8 1.0
OD2 A:ASP10 3.4 10.4 1.0
C A:LEU9 3.5 7.9 1.0
CG A:ASP8 3.5 9.2 1.0
CG A:ASP10 3.6 8.9 1.0
CA A:SER114 3.6 11.7 1.0
CB A:ASP10 3.8 8.8 1.0
CA A:ASP10 3.8 8.4 1.0
OD2 A:ASP8 4.0 9.4 1.0
C A:ASP8 4.1 8.8 1.0
C1 A:BG6301 4.1 10.8 1.0
N A:ALA115 4.3 12.0 1.0
OD1 A:ASP10 4.3 10.0 1.0
MG A:MG302 4.4 9.3 1.0
CA A:ASP8 4.4 9.1 1.0
C A:SER114 4.5 10.9 1.0
O A:ASP10 4.6 9.5 1.0
CB A:ASP8 4.6 10.1 1.0
CG A:LEU9 4.6 10.5 1.0
O A:LEU9 4.7 8.9 1.0
C A:ASP10 4.7 8.7 1.0
N A:SER116 4.7 9.9 1.0
CB A:SER116 4.7 10.1 1.0
O5 A:BG6301 4.8 10.8 1.0
N A:SER114 4.8 11.3 1.0
O2 A:BG6301 4.8 10.8 1.0
C2 A:BG6301 4.9 10.4 1.0
NZ A:LYS145 5.0 10.8 1.0

Fluorine binding site 3 out of 3 in 6hdl

Go back to Fluorine Binding Sites List in 6hdl
Fluorine binding site 3 out of 3 in the R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of R49K Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.2 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:13.4
occ:1.00
F3 A:MGF303 0.0 13.4 1.0
MG A:MGF303 1.8 12.1 1.0
NZ A:LYS145 2.6 10.8 1.0
O1 A:BG6301 2.7 11.2 1.0
OD1 A:ASP8 2.7 9.7 1.0
N A:ALA115 2.8 12.0 1.0
F1 A:MGF303 3.2 10.3 1.0
F2 A:MGF303 3.2 10.5 1.0
C1 A:BG6301 3.2 10.8 1.0
CB A:ALA115 3.4 15.5 1.0
CE A:LYS145 3.5 12.0 1.0
CA A:ALA115 3.7 12.5 1.0
C A:SER114 3.7 10.9 1.0
CA A:SER114 3.7 11.7 1.0
O A:HOH478 3.9 10.6 1.0
CG A:ASP8 3.9 9.2 1.0
CA A:GLY46 3.9 10.4 1.0
CD A:LYS145 3.9 12.8 1.0
O2 A:BG6301 4.1 10.8 1.0
OG A:SER114 4.1 10.6 1.0
O A:GLY46 4.1 12.3 1.0
O5 A:BG6301 4.2 10.8 1.0
C2 A:BG6301 4.3 10.4 1.0
O A:ALA113 4.4 12.2 1.0
C A:GLY46 4.4 10.2 1.0
CB A:SER114 4.5 10.9 1.0
OE2 A:GLU169 4.5 13.9 1.0
OD2 A:ASP8 4.5 9.4 1.0
N A:SER116 4.5 9.9 1.0
C A:ALA115 4.6 10.1 1.0
MG A:MG302 4.6 9.3 1.0
N A:GLY46 4.9 10.3 1.0
N A:SER114 4.9 11.3 1.0
O A:SER114 4.9 14.3 1.0
CB A:ASP8 5.0 10.1 1.0

Reference:

A.J.Robertson, C.Bisson, J.P.Waltho. Transition State of Phospho-Enzyme Hydrolysis in Beta-Phosphoglucomutase. To Be Published.
Page generated: Sun Dec 13 12:52:44 2020

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