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:
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
|