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:
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
|