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Fluorine in PDB 6hdm: R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A.

Enzymatic activity of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A.

All present enzymatic activity of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A.:
5.4.2.6;

Protein crystallography data

The structure of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A., PDB code: 6hdm was solved by 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) 48.27 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.300, 54.340, 104.620, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.8

Other elements in 6hdm:

The structure of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 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 R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A. (pdb code 6hdm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A., PDB code: 6hdm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6hdm

Go back to Fluorine Binding Sites List in 6hdm
Fluorine binding site 1 out of 3 in the R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:15.2
occ:1.00
 F1 A:MGF302 0.0 15.2 1.0
MG A:MGF302 1.9 8.1 1.0
NZ A:LYS145 2.6 10.6 1.0
O1 A:BG6304 2.8 8.1 1.0
OD1 A:ASP8 2.8 8.4 1.0
N A:ALA115 2.8 13.3 1.0
C1 A:BG6304 3.2 8.2 1.0
CB A:ALA115 3.3 17.2 1.0
F3 A:MGF302 3.4 8.6 1.0
F2 A:MGF302 3.4 8.3 1.0
CE A:LYS145 3.4 11.0 1.0
CA A:ALA115 3.6 13.4 1.0
C A:SER114 3.7 11.3 1.0
CA A:SER114 3.7 12.6 1.0
CD A:LYS145 3.8 11.5 1.0
O A:HOH495 3.9 10.4 1.0
CG A:ASP8 4.0 8.2 1.0
O A:GLY46 4.1 11.9 1.0
CA A:GLY46 4.1 10.7 1.0
OG A:SER114 4.1 10.2 1.0
O2 A:BG6304 4.1 9.0 1.0
O5 A:BG6304 4.2 8.2 1.0
O A:ALA113 4.3 11.6 1.0
C2 A:BG6304 4.3 8.5 1.0
C A:GLY46 4.5 10.2 1.0
OE2 A:GLU169 4.5 14.8 1.0
CB A:SER114 4.5 10.6 1.0
C A:ALA115 4.5 10.8 1.0
N A:SER116 4.5 9.4 1.0
OD2 A:ASP8 4.6 8.6 1.0
MG A:MG301 4.7 8.4 1.0
N A:SER114 4.8 11.0 1.0
O A:SER114 4.9 14.8 1.0

Fluorine binding site 2 out of 3 in 6hdm

Go back to Fluorine Binding Sites List in 6hdm
Fluorine binding site 2 out of 3 in the R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:8.3
occ:1.00
 F2 A:MGF302 0.0 8.3 1.0
MG A:MGF302 1.9 8.1 1.0
OG A:SER114 2.6 10.2 1.0
N A:ASP10 2.7 7.2 1.0
O1 A:BG6304 2.8 8.1 1.0
OD1 A:ASP8 2.8 8.4 1.0
N A:LEU9 2.9 7.5 1.0
F3 A:MGF302 3.0 8.6 1.0
CB A:SER114 3.2 10.6 1.0
CB A:LEU9 3.2 8.1 1.0
CA A:LEU9 3.3 7.1 1.0
OD2 A:ASP10 3.3 8.6 1.0
F1 A:MGF302 3.4 15.2 1.0
C A:LEU9 3.5 7.0 1.0
CG A:ASP10 3.5 8.0 1.0
CG A:ASP8 3.6 8.2 1.0
CA A:SER114 3.7 12.6 1.0
CB A:ASP10 3.8 7.2 1.0
CA A:ASP10 3.8 7.0 1.0
OD2 A:ASP8 4.0 8.6 1.0
C A:ASP8 4.1 7.7 1.0
C1 A:BG6304 4.2 8.2 1.0
OD1 A:ASP10 4.2 8.2 1.0
N A:ALA115 4.4 13.3 1.0
CA A:ASP8 4.5 8.1 1.0
MG A:MG301 4.5 8.4 1.0
C A:SER114 4.5 11.3 1.0
O A:ASP10 4.6 8.1 1.0
CG A:LEU9 4.6 8.2 1.0
CB A:ASP8 4.6 8.2 1.0
O A:LEU9 4.7 8.0 1.0
C A:ASP10 4.7 6.8 1.0
CB A:SER116 4.7 8.8 1.0
N A:SER116 4.8 9.4 1.0
N A:SER114 4.8 11.0 1.0
O5 A:BG6304 4.8 8.2 1.0
O2 A:BG6304 4.9 9.0 1.0
C2 A:BG6304 4.9 8.5 1.0
CD2 A:LEU9 4.9 8.8 1.0

Fluorine binding site 3 out of 3 in 6hdm

Go back to Fluorine Binding Sites List in 6hdm
Fluorine binding site 3 out of 3 in the R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Magnesium Trifluoride and Beta-G6P to 1.3 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:8.6
occ:1.00
 F3 A:MGF302 0.0 8.6 1.0
MG A:MGF302 1.9 8.1 1.0
MG A:MG301 1.9 8.4 1.0
O2 A:BG6304 2.6 9.0 1.0
O A:HOH495 2.8 10.4 1.0
O1 A:BG6304 2.8 8.1 1.0
OD2 A:ASP8 2.9 8.6 1.0
O A:ASP10 2.9 8.1 1.0
O A:HOH435 2.9 8.6 1.0
OD1 A:ASP8 3.0 8.4 1.0
F2 A:MGF302 3.0 8.3 1.0
CB A:ASP10 3.2 7.2 1.0
CG A:ASP8 3.3 8.2 1.0
F1 A:MGF302 3.4 15.2 1.0
C2 A:BG6304 3.4 8.5 1.0
N A:ASP10 3.5 7.2 1.0
C1 A:BG6304 3.5 8.2 1.0
CA A:ASP10 3.6 7.0 1.0
C A:ASP10 3.6 6.8 1.0
OD2 A:ASP10 3.8 8.6 1.0
CG A:ASP10 3.9 8.0 1.0
OD1 A:ASP170 4.0 8.7 1.0
O A:HOH512 4.3 10.4 1.0
N A:GLY46 4.5 10.1 1.0
CA A:GLY46 4.5 10.7 1.0
C A:LEU9 4.5 7.0 1.0
N A:LEU9 4.7 7.5 1.0
CB A:ASP8 4.8 8.2 1.0
O5 A:BG6304 4.8 8.2 1.0
C3 A:BG6304 4.8 9.1 1.0
CG A:ASP170 4.9 8.5 1.0
N A:GLY11 4.9 7.1 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: Tue Jul 15 12:13:58 2025

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