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Fluorine in PDB 5ok2: Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution.

Enzymatic activity of Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution.

All present enzymatic activity of Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution.:
5.4.2.6;

Protein crystallography data

The structure of Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution., PDB code: 5ok2 was solved by A.J.Robertson, C.Bisson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.39 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.540, 54.280, 104.670, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17

Other elements in 5ok2:

The structure of Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution. also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution. (pdb code 5ok2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution., PDB code: 5ok2:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5ok2

Go back to Fluorine Binding Sites List in 5ok2
Fluorine binding site 1 out of 4 in the Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:8.2
occ:1.00
F1 A:ALF301 0.0 8.2 1.0
AL A:ALF301 1.8 8.2 1.0
MG A:MG308 2.0 8.1 1.0
F2 A:ALF301 2.5 8.9 1.0
F4 A:ALF301 2.6 8.4 1.0
O1 A:BG6310 2.6 8.3 1.0
OD1 A:ASP8 2.7 8.4 1.0
O2 A:BG6310 2.8 8.8 1.0
OD2 A:ASP8 2.8 8.6 1.0
O A:HOH431 2.9 9.5 1.0
O A:ASN10 3.0 8.5 1.0
O A:HOH463 3.0 9.3 1.0
CG A:ASP8 3.1 8.2 1.0
CB A:ASN10 3.2 8.1 1.0
N A:ASN10 3.3 7.7 1.0
C1 A:BG6310 3.5 8.2 1.0
C2 A:BG6310 3.5 8.7 1.0
CA A:ASN10 3.5 7.9 1.0
F3 A:ALF301 3.6 9.3 1.0
ND2 A:ASN10 3.6 8.2 1.0
C A:ASN10 3.6 7.4 1.0
CG A:ASN10 3.9 8.1 1.0
OD1 A:ASP170 4.1 8.5 1.0
C A:LEU9 4.3 7.0 0.5
C A:LEU9 4.4 7.4 0.5
N A:LEU9 4.4 8.0 0.5
O A:HOH537 4.4 10.3 1.0
N A:LEU9 4.4 7.7 0.5
CB A:ASP8 4.6 8.2 1.0
O5 A:BG6310 4.7 8.2 1.0
N A:GLY46 4.7 9.5 1.0
CA A:GLY46 4.8 10.3 1.0
CA A:LEU9 4.9 8.0 0.5
C3 A:BG6310 4.9 9.1 1.0
CA A:LEU9 4.9 7.3 0.5
N A:GLY11 5.0 7.7 1.0

Fluorine binding site 2 out of 4 in 5ok2

Go back to Fluorine Binding Sites List in 5ok2
Fluorine binding site 2 out of 4 in the Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:8.9
occ:1.00
F2 A:ALF301 0.0 8.9 1.0
AL A:ALF301 1.8 8.2 1.0
F3 A:ALF301 2.5 9.3 1.0
F1 A:ALF301 2.5 8.2 1.0
O A:HOH431 2.6 9.5 1.0
OD1 A:ASP8 2.7 8.4 1.0
O1 A:BG6310 2.7 8.3 1.0
NZ A:LYS145 3.1 10.2 1.0
CA A:GLY46 3.1 10.3 1.0
C1 A:BG6310 3.1 8.2 1.0
O2 A:BG6310 3.2 8.8 1.0
F4 A:ALF301 3.6 8.4 1.0
CG A:ASP8 3.6 8.2 1.0
MG A:MG308 3.6 8.1 1.0
N A:GLY46 3.7 9.5 1.0
C2 A:BG6310 3.8 8.7 1.0
C A:GLY46 3.9 10.1 1.0
OD2 A:ASP8 3.9 8.6 1.0
CE A:LYS145 4.0 11.3 1.0
O A:GLY46 4.0 12.7 1.0
CD A:LYS145 4.0 11.9 1.0
OE2 A:GLU169 4.0 12.4 1.0
O5 A:BG6310 4.4 8.2 1.0
O A:HOH463 4.5 9.3 1.0
OE1 A:GLU169 4.6 11.9 1.0
CB A:ALA115 4.6 11.0 1.0
CD A:GLU169 4.7 11.1 1.0
N A:ALA115 4.7 9.0 1.0
OG A:SER171 4.7 11.1 1.0
CB A:ASP8 4.8 8.2 1.0
C3 A:BG6310 4.8 9.1 1.0
C A:LYS45 5.0 8.8 1.0

Fluorine binding site 3 out of 4 in 5ok2

Go back to Fluorine Binding Sites List in 5ok2
Fluorine binding site 3 out of 4 in the Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:9.3
occ:1.00
F3 A:ALF301 0.0 9.3 1.0
AL A:ALF301 1.8 8.2 1.0
F2 A:ALF301 2.5 8.9 1.0
F4 A:ALF301 2.5 8.4 1.0
OD1 A:ASP8 2.6 8.4 1.0
N A:ALA115 2.6 9.0 1.0
O1 A:BG6310 2.7 8.3 1.0
NZ A:LYS145 2.8 10.2 1.0
CA A:SER114 3.0 8.7 1.0
OG A:SER114 3.1 8.9 1.0
C A:SER114 3.3 9.1 1.0
CB A:SER114 3.5 8.9 1.0
C1 A:BG6310 3.6 8.2 1.0
F1 A:ALF301 3.6 8.2 1.0
CE A:LYS145 3.7 11.3 1.0
CA A:ALA115 3.7 9.1 1.0
CB A:ALA115 3.7 11.0 1.0
CG A:ASP8 3.8 8.2 1.0
O A:ALA113 3.8 10.7 1.0
N A:SER114 4.2 9.1 1.0
O5 A:BG6310 4.2 8.2 1.0
N A:SER116 4.2 8.5 1.0
C A:ALA113 4.4 9.5 1.0
C A:ALA115 4.5 9.2 1.0
O A:SER114 4.5 10.8 1.0
CD A:LYS145 4.5 11.9 1.0
N A:LEU9 4.5 8.0 0.5
N A:LEU9 4.5 7.7 0.5
CB A:ASP8 4.7 8.2 1.0
OD2 A:ASP8 4.7 8.6 1.0
CA A:ASP8 4.7 8.1 1.0
O A:HOH431 4.8 9.5 1.0
ND2 A:ASN10 4.8 8.2 1.0
C2 A:BG6310 4.8 8.7 1.0
O2 A:BG6310 4.9 8.8 1.0
OE2 A:GLU169 4.9 12.4 1.0

Fluorine binding site 4 out of 4 in 5ok2

Go back to Fluorine Binding Sites List in 5ok2
Fluorine binding site 4 out of 4 in the Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the D10N Mutant of Beta-Phosphoglucomutase From Lactococcus Lactis Inhibited with Glucose 6-Phosphate and Tetrafluoroaluminate to 1.1A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:8.4
occ:1.00
F4 A:ALF301 0.0 8.4 1.0
AL A:ALF301 1.8 8.2 1.0
O1 A:BG6310 2.5 8.3 1.0
F3 A:ALF301 2.5 9.3 1.0
F1 A:ALF301 2.6 8.2 1.0
OD1 A:ASP8 2.6 8.4 1.0
OG A:SER114 2.8 8.9 1.0
N A:ASN10 2.8 7.7 1.0
N A:LEU9 2.9 8.0 0.5
N A:LEU9 2.9 7.7 0.5
ND2 A:ASN10 3.0 8.2 1.0
CB A:LEU9 3.2 9.1 0.5
CA A:LEU9 3.3 8.0 0.5
CG A:ASP8 3.4 8.2 1.0
CA A:LEU9 3.4 7.3 0.5
CB A:LEU9 3.4 7.5 0.5
C A:LEU9 3.5 7.4 0.5
CB A:SER114 3.5 8.9 1.0
C A:LEU9 3.5 7.0 0.5
F2 A:ALF301 3.6 8.9 1.0
CG A:ASN10 3.6 8.1 1.0
CB A:ASN10 3.8 8.1 1.0
OD2 A:ASP8 3.8 8.6 1.0
CA A:ASN10 3.9 7.9 1.0
C1 A:BG6310 3.9 8.2 1.0
C A:ASP8 4.0 8.0 1.0
CA A:SER114 4.1 8.7 1.0
MG A:MG308 4.2 8.1 1.0
CG A:LEU9 4.3 10.3 0.5
CA A:ASP8 4.3 8.1 1.0
CB A:ASP8 4.4 8.2 1.0
O A:ASN10 4.5 8.5 1.0
O5 A:BG6310 4.5 8.2 1.0
OD1 A:ASN10 4.5 9.2 1.0
N A:ALA115 4.5 9.0 1.0
C2 A:BG6310 4.6 8.7 1.0
CD2 A:LEU9 4.7 10.9 0.5
C A:ASN10 4.7 7.4 1.0
O2 A:BG6310 4.7 8.8 1.0
O A:LEU9 4.7 8.2 0.5
O A:LEU9 4.7 7.8 0.5
CG A:LEU9 4.8 7.7 0.5
NZ A:LYS145 4.8 10.2 1.0
C A:SER114 4.8 9.1 1.0
CB A:SER116 4.9 8.4 1.0
O A:HOH431 4.9 9.5 1.0
N A:SER116 5.0 8.5 1.0

Reference:

L.A.Johnson, A.J.Robertson, N.J.Baxter, C.R.Trevitt, C.Bisson, Y.Jin, H.P.Wood, A.M.Hounslow, M.J.Cliff, G.M.Blackburn, M.W.Bowler, J.P.Waltho. Van Der Waals Contact Between Nucleophile and Transferring Phosphorus Is Insufficient to Achieve Enzyme Transition-State Architecture Acs Catalysis 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B01612
Page generated: Thu Aug 1 12:28:53 2024

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