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Fluorine in PDB 6i03: D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A

Enzymatic activity of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A

All present enzymatic activity of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A:
5.4.2.6;

Protein crystallography data

The structure of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A, PDB code: 6i03 was solved by A.J.Robertson, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.33 / 1.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.520, 54.280, 104.420, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.5

Other elements in 6i03:

The structure of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A (pdb code 6i03). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A, PDB code: 6i03:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6i03

Go back to Fluorine Binding Sites List in 6i03
Fluorine binding site 1 out of 4 in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:10.5
occ:1.00
 F1 A:ALF301 0.0 10.5 1.0
AL A:ALF301 1.8 11.3 1.0
MG A:MG304 2.0 10.3 1.0
F4 A:ALF301 2.5 12.6 1.0
O1 A:BG6302 2.6 11.0 1.0
F3 A:ALF301 2.6 10.4 1.0
OD1 A:ASP8 2.7 10.5 1.0
O2 A:BG6302 2.8 11.5 1.0
OD2 A:ASP8 2.8 11.3 1.0
O A:HOH440 2.8 12.8 1.0
O A:ASN10 2.9 10.3 1.0
O A:HOH451 3.0 11.7 1.0
CG A:ASP8 3.1 10.3 1.0
CB A:ASN10 3.2 9.8 1.0
N A:ASN10 3.3 8.5 1.0
C1 A:BG6302 3.4 11.1 1.0
C2 A:BG6302 3.5 11.3 1.0
CA A:ASN10 3.6 8.9 1.0
F2 A:ALF301 3.6 12.6 1.0
C A:ASN10 3.7 8.9 1.0
ND2 A:ASN10 3.7 11.3 1.0
CG A:ASN10 3.9 10.0 1.0
OD1 A:ASP170 4.1 10.7 1.0
C A:LEU9 4.4 8.1 1.0
O A:HOH509 4.4 12.1 1.0
N A:LEU9 4.4 8.8 1.0
CB A:ASP8 4.6 11.3 1.0
N A:GLY46 4.6 12.7 1.0
O5 A:BG6302 4.7 10.9 1.0
CA A:GLY46 4.7 13.1 1.0
NZ A:LYS145 4.8 9.4 0.5
C3 A:BG6302 4.9 11.6 1.0
N A:GLY11 5.0 8.9 1.0
CA A:LEU9 5.0 9.1 1.0
CG A:ASP170 5.0 10.7 1.0

Fluorine binding site 2 out of 4 in 6i03

Go back to Fluorine Binding Sites List in 6i03
Fluorine binding site 2 out of 4 in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:12.6
occ:1.00
 F2 A:ALF301 0.0 12.6 1.0
AL A:ALF301 1.8 11.3 1.0
F4 A:ALF301 2.5 12.6 1.0
F3 A:ALF301 2.6 10.4 1.0
OD1 A:ASP8 2.6 10.5 1.0
N A:ALA115 2.6 11.6 1.0
NZ A:LYS145 2.7 9.8 0.5
O1 A:BG6302 2.7 11.0 1.0
NZ A:LYS145 2.9 9.4 0.5
CA A:SER114 2.9 11.6 1.0
OG A:SER114 3.1 10.8 1.0
C A:SER114 3.2 11.9 1.0
CB A:SER114 3.5 10.6 1.0
C1 A:BG6302 3.6 11.1 1.0
F1 A:ALF301 3.6 10.5 1.0
CE A:LYS145 3.6 9.6 0.5
CA A:ALA115 3.7 11.7 1.0
CB A:ALA115 3.7 14.6 1.0
CE A:LYS145 3.8 9.6 0.5
CG A:ASP8 3.8 10.3 1.0
O A:ALA113 3.8 13.9 1.0
N A:SER114 4.2 11.9 1.0
O5 A:BG6302 4.2 10.9 1.0
N A:SER116 4.2 11.4 1.0
CD A:LYS145 4.3 9.6 0.5
C A:ALA113 4.4 12.7 1.0
O A:SER114 4.5 12.9 1.0
C A:ALA115 4.5 11.4 1.0
N A:LEU9 4.5 8.8 1.0
OD2 A:ASP8 4.7 11.3 1.0
CD A:LYS145 4.7 10.0 0.5
CB A:ASP8 4.7 11.3 1.0
O A:HOH440 4.7 12.8 1.0
CA A:ASP8 4.7 10.2 1.0
ND2 A:ASN10 4.8 11.3 1.0
C2 A:BG6302 4.8 11.3 1.0
O2 A:BG6302 4.9 11.5 1.0
OE2 A:GLU169 4.9 15.7 1.0

Fluorine binding site 3 out of 4 in 6i03

Go back to Fluorine Binding Sites List in 6i03
Fluorine binding site 3 out of 4 in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:10.4
occ:1.00
 F3 A:ALF301 0.0 10.4 1.0
AL A:ALF301 1.8 11.3 1.0
O1 A:BG6302 2.5 11.0 1.0
F2 A:ALF301 2.6 12.6 1.0
OD1 A:ASP8 2.6 10.5 1.0
F1 A:ALF301 2.6 10.5 1.0
OG A:SER114 2.8 10.8 1.0
N A:ASN10 2.8 8.5 1.0
N A:LEU9 2.9 8.8 1.0
ND2 A:ASN10 3.0 11.3 1.0
CB A:LEU9 3.3 9.5 1.0
CA A:LEU9 3.4 9.1 1.0
CG A:ASP8 3.4 10.3 1.0
C A:LEU9 3.5 8.1 1.0
CB A:SER114 3.5 10.6 1.0
F4 A:ALF301 3.6 12.6 1.0
CG A:ASN10 3.6 10.0 1.0
OD2 A:ASP8 3.8 11.3 1.0
CB A:ASN10 3.8 9.8 1.0
CA A:ASN10 3.9 8.9 1.0
C1 A:BG6302 3.9 11.1 1.0
C A:ASP8 4.0 9.0 1.0
CA A:SER114 4.0 11.6 1.0
MG A:MG304 4.2 10.3 1.0
CA A:ASP8 4.3 10.2 1.0
CB A:ASP8 4.4 11.3 1.0
O A:ASN10 4.5 10.3 1.0
N A:ALA115 4.5 11.6 1.0
OD1 A:ASN10 4.5 10.9 1.0
O5 A:BG6302 4.6 10.9 1.0
C2 A:BG6302 4.7 11.3 1.0
C A:ASN10 4.7 8.9 1.0
CG A:LEU9 4.7 13.0 1.0
O2 A:BG6302 4.7 11.5 1.0
O A:LEU9 4.7 8.8 1.0
NZ A:LYS145 4.8 9.8 0.5
C A:SER114 4.8 11.9 1.0
NZ A:LYS145 4.8 9.4 0.5
CB A:SER116 4.9 10.4 1.0
O A:HOH440 4.9 12.8 1.0
N A:SER116 5.0 11.4 1.0

Fluorine binding site 4 out of 4 in 6i03

Go back to Fluorine Binding Sites List in 6i03
Fluorine binding site 4 out of 4 in the D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of D10N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Tetrafluoroaluminate and Beta-G6P to 1.02 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:12.6
occ:1.00
 F4 A:ALF301 0.0 12.6 1.0
AL A:ALF301 1.8 11.3 1.0
F2 A:ALF301 2.5 12.6 1.0
F1 A:ALF301 2.5 10.5 1.0
O A:HOH440 2.6 12.8 1.0
OD1 A:ASP8 2.6 10.5 1.0
O1 A:BG6302 2.7 11.0 1.0
NZ A:LYS145 2.9 9.4 0.5
CA A:GLY46 3.0 13.1 1.0
C1 A:BG6302 3.1 11.1 1.0
O2 A:BG6302 3.2 11.5 1.0
NZ A:LYS145 3.2 9.8 0.5
CG A:ASP8 3.6 10.3 1.0
F3 A:ALF301 3.6 10.4 1.0
MG A:MG304 3.6 10.3 1.0
N A:GLY46 3.7 12.7 1.0
CE A:LYS145 3.8 9.6 0.5
C2 A:BG6302 3.8 11.3 1.0
OD2 A:ASP8 3.9 11.3 1.0
CD A:LYS145 3.9 10.0 0.5
C A:GLY46 3.9 12.1 1.0
O A:GLY46 4.0 14.9 1.0
OE2 A:GLU169 4.0 15.7 1.0
CD A:LYS145 4.0 9.6 0.5
CE A:LYS145 4.1 9.6 0.5
O5 A:BG6302 4.4 10.9 1.0
O A:HOH451 4.5 11.7 1.0
OE1 A:GLU169 4.5 15.6 1.0
CB A:ALA115 4.6 14.6 1.0
N A:ALA115 4.6 11.6 1.0
CD A:GLU169 4.7 15.0 1.0
OG A:SER171 4.7 15.3 1.0
CB A:ASP8 4.8 11.3 1.0
C3 A:BG6302 4.9 11.6 1.0
C A:LYS45 4.9 12.0 1.0

Reference:

A.J.Robertson, C.Bisson, J.P.Waltho. Proton Transfer Modulates the Electrostatic Environment in A General Acid-Base Catalyzed Phosphoryl Transfer Reaction To Be Published.
Page generated: Tue Jul 15 12:26:47 2025

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