Fluorine in PDB 7ziy: X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
Enzymatic activity of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
All present enzymatic activity of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5):
3.8.1.5;
Protein crystallography data
The structure of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5), PDB code: 7ziy
was solved by
M.Tarnawski,
J.Kompa,
K.Johnsson,
J.Hiblot,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.40 /
1.70
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.24,
46.06,
79.06,
94.41,
90,
109.51
|
R / Rfree (%)
|
19.1 /
22.4
|
Other elements in 7ziy:
The structure of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5) also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
(pdb code 7ziy). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5), PDB code: 7ziy:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 7ziy
Go back to
Fluorine Binding Sites List in 7ziy
Fluorine binding site 1 out
of 6 in the X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:24.6
occ:1.00
|
F
|
A:IYI301
|
0.0
|
24.6
|
1.0
|
C10
|
A:IYI301
|
1.3
|
28.2
|
1.0
|
F2
|
A:IYI301
|
2.1
|
25.0
|
1.0
|
F1
|
A:IYI301
|
2.1
|
25.7
|
1.0
|
S
|
A:IYI301
|
2.6
|
20.4
|
1.0
|
N1
|
A:IYI301
|
2.9
|
21.7
|
1.0
|
O3
|
A:IYI301
|
3.0
|
22.5
|
1.0
|
NE1
|
A:TRP107
|
3.3
|
19.1
|
1.0
|
CD1
|
A:ILE132
|
3.3
|
18.6
|
1.0
|
C9
|
A:IYI301
|
3.6
|
22.2
|
1.0
|
O4
|
A:IYI301
|
3.7
|
24.4
|
1.0
|
CD1
|
A:TRP107
|
3.7
|
17.2
|
1.0
|
OD2
|
A:ASP106
|
3.9
|
20.0
|
1.0
|
CD2
|
A:LEU246
|
3.9
|
20.1
|
1.0
|
CD1
|
A:LEU246
|
4.0
|
19.5
|
1.0
|
CD1
|
A:LEU209
|
4.1
|
22.7
|
1.0
|
CE2
|
A:TRP107
|
4.1
|
16.9
|
1.0
|
OD1
|
A:ASP106
|
4.3
|
20.2
|
1.0
|
CG
|
A:ASP106
|
4.3
|
20.4
|
1.0
|
CG
|
A:LEU246
|
4.6
|
15.3
|
1.0
|
CZ2
|
A:TRP107
|
4.7
|
16.0
|
1.0
|
CB
|
A:LEU209
|
4.7
|
15.4
|
1.0
|
CG
|
A:TRP107
|
4.7
|
14.4
|
1.0
|
CG1
|
A:ILE132
|
4.8
|
19.3
|
1.0
|
CG
|
A:LEU209
|
4.9
|
20.2
|
1.0
|
CD2
|
A:TRP107
|
4.9
|
14.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 7ziy
Go back to
Fluorine Binding Sites List in 7ziy
Fluorine binding site 2 out
of 6 in the X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:25.7
occ:1.00
|
F1
|
A:IYI301
|
0.0
|
25.7
|
1.0
|
C10
|
A:IYI301
|
1.3
|
28.2
|
1.0
|
F
|
A:IYI301
|
2.1
|
24.6
|
1.0
|
F2
|
A:IYI301
|
2.2
|
25.0
|
1.0
|
S
|
A:IYI301
|
2.6
|
20.4
|
1.0
|
O4
|
A:IYI301
|
2.9
|
24.4
|
1.0
|
N1
|
A:IYI301
|
3.1
|
21.7
|
1.0
|
C9
|
A:IYI301
|
3.1
|
22.2
|
1.0
|
CH2
|
A:TRP141
|
3.5
|
23.8
|
1.0
|
CD2
|
A:LEU246
|
3.6
|
20.1
|
1.0
|
O3
|
A:IYI301
|
3.7
|
22.5
|
1.0
|
CD1
|
A:LEU209
|
3.8
|
22.7
|
1.0
|
CD2
|
A:LEU209
|
3.8
|
21.3
|
1.0
|
CE2
|
A:PHE149
|
4.0
|
19.4
|
1.0
|
CG
|
A:LEU209
|
4.2
|
20.2
|
1.0
|
CZ3
|
A:TRP141
|
4.3
|
21.4
|
1.0
|
CB
|
A:LEU209
|
4.3
|
15.4
|
1.0
|
CZ2
|
A:TRP141
|
4.4
|
20.8
|
1.0
|
C8
|
A:IYI301
|
4.5
|
24.6
|
1.0
|
CG
|
A:LEU246
|
4.6
|
15.3
|
1.0
|
CD2
|
A:PHE149
|
4.7
|
16.9
|
1.0
|
CD1
|
A:LEU246
|
4.7
|
19.5
|
1.0
|
CZ
|
A:PHE149
|
4.8
|
22.9
|
1.0
|
NE1
|
A:TRP107
|
4.9
|
19.1
|
1.0
|
OD2
|
A:ASP106
|
5.0
|
20.0
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 7ziy
Go back to
Fluorine Binding Sites List in 7ziy
Fluorine binding site 3 out
of 6 in the X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:25.0
occ:1.00
|
F2
|
A:IYI301
|
0.0
|
25.0
|
1.0
|
C10
|
A:IYI301
|
1.3
|
28.2
|
1.0
|
F
|
A:IYI301
|
2.1
|
24.6
|
1.0
|
F1
|
A:IYI301
|
2.2
|
25.7
|
1.0
|
S
|
A:IYI301
|
2.6
|
20.4
|
1.0
|
O3
|
A:IYI301
|
2.9
|
22.5
|
1.0
|
O4
|
A:IYI301
|
3.1
|
24.4
|
1.0
|
CB
|
A:LEU209
|
3.2
|
15.4
|
1.0
|
NE1
|
A:TRP107
|
3.3
|
19.1
|
1.0
|
O
|
A:PHE205
|
3.5
|
15.2
|
1.0
|
CA
|
A:PRO206
|
3.6
|
14.9
|
1.0
|
CD1
|
A:LEU209
|
3.8
|
22.7
|
1.0
|
N1
|
A:IYI301
|
3.8
|
21.7
|
1.0
|
CG
|
A:LEU209
|
3.9
|
20.2
|
1.0
|
CA
|
A:LEU209
|
4.1
|
17.3
|
1.0
|
C
|
A:PHE205
|
4.1
|
13.7
|
1.0
|
N
|
A:PRO206
|
4.1
|
15.3
|
1.0
|
CE2
|
A:TRP107
|
4.1
|
16.9
|
1.0
|
CD2
|
A:LEU209
|
4.1
|
21.3
|
1.0
|
CD1
|
A:TRP107
|
4.3
|
17.2
|
1.0
|
CZ2
|
A:TRP107
|
4.3
|
16.0
|
1.0
|
N
|
A:LEU209
|
4.4
|
16.6
|
1.0
|
CB
|
A:PRO206
|
4.5
|
17.6
|
1.0
|
C
|
A:PRO206
|
4.5
|
14.9
|
1.0
|
O
|
A:PRO206
|
4.5
|
17.0
|
1.0
|
C9
|
A:IYI301
|
4.6
|
22.2
|
1.0
|
CD1
|
A:ILE132
|
4.9
|
18.6
|
1.0
|
CD
|
A:PRO206
|
4.9
|
19.2
|
1.0
|
CE2
|
A:PHE149
|
5.0
|
19.4
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 7ziy
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Fluorine Binding Sites List in 7ziy
Fluorine binding site 4 out
of 6 in the X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F302
b:26.2
occ:1.00
|
F
|
B:IYI302
|
0.0
|
26.2
|
1.0
|
C10
|
B:IYI302
|
1.3
|
25.8
|
1.0
|
F1
|
B:IYI302
|
2.1
|
26.8
|
1.0
|
F2
|
B:IYI302
|
2.1
|
25.0
|
1.0
|
S
|
B:IYI302
|
2.6
|
21.0
|
1.0
|
N1
|
B:IYI302
|
2.9
|
24.0
|
1.0
|
O3
|
B:IYI302
|
3.0
|
23.1
|
1.0
|
CD1
|
B:ILE132
|
3.3
|
18.0
|
1.0
|
NE1
|
B:TRP107
|
3.3
|
18.5
|
1.0
|
C9
|
B:IYI302
|
3.6
|
27.2
|
1.0
|
O4
|
B:IYI302
|
3.7
|
23.6
|
1.0
|
CD1
|
B:TRP107
|
3.8
|
18.0
|
1.0
|
OD2
|
B:ASP106
|
3.8
|
21.9
|
1.0
|
CD1
|
B:LEU209
|
3.9
|
22.1
|
1.0
|
CD1
|
B:LEU246
|
3.9
|
18.4
|
1.0
|
CD2
|
B:LEU246
|
4.0
|
24.3
|
1.0
|
CE2
|
B:TRP107
|
4.1
|
15.7
|
1.0
|
OD1
|
B:ASP106
|
4.2
|
18.0
|
1.0
|
CG
|
B:ASP106
|
4.3
|
20.2
|
1.0
|
CG
|
B:LEU246
|
4.5
|
18.9
|
1.0
|
CZ2
|
B:TRP107
|
4.7
|
15.6
|
1.0
|
CG
|
B:TRP107
|
4.7
|
12.8
|
1.0
|
CG1
|
B:ILE132
|
4.7
|
15.6
|
1.0
|
CG
|
B:LEU209
|
4.8
|
16.8
|
1.0
|
CB
|
B:LEU209
|
4.8
|
13.9
|
1.0
|
CD2
|
B:TRP107
|
4.9
|
14.2
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 7ziy
Go back to
Fluorine Binding Sites List in 7ziy
Fluorine binding site 5 out
of 6 in the X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F302
b:26.8
occ:1.00
|
F1
|
B:IYI302
|
0.0
|
26.8
|
1.0
|
C10
|
B:IYI302
|
1.3
|
25.8
|
1.0
|
F
|
B:IYI302
|
2.1
|
26.2
|
1.0
|
F2
|
B:IYI302
|
2.2
|
25.0
|
1.0
|
S
|
B:IYI302
|
2.6
|
21.0
|
1.0
|
O4
|
B:IYI302
|
2.9
|
23.6
|
1.0
|
C9
|
B:IYI302
|
3.1
|
27.2
|
1.0
|
N1
|
B:IYI302
|
3.1
|
24.0
|
1.0
|
CH2
|
B:TRP141
|
3.6
|
21.4
|
1.0
|
CD1
|
B:LEU209
|
3.6
|
22.1
|
1.0
|
O3
|
B:IYI302
|
3.7
|
23.1
|
1.0
|
CD2
|
B:LEU246
|
3.7
|
24.3
|
1.0
|
CD2
|
B:LEU209
|
3.8
|
22.4
|
1.0
|
CE2
|
B:PHE149
|
4.1
|
18.2
|
1.0
|
CG
|
B:LEU209
|
4.1
|
16.8
|
1.0
|
CZ3
|
B:TRP141
|
4.3
|
21.4
|
1.0
|
CB
|
B:LEU209
|
4.4
|
13.9
|
1.0
|
C8
|
B:IYI302
|
4.5
|
24.4
|
1.0
|
CZ2
|
B:TRP141
|
4.5
|
20.4
|
1.0
|
CG
|
B:LEU246
|
4.5
|
18.9
|
1.0
|
CD1
|
B:LEU246
|
4.6
|
18.4
|
1.0
|
CD2
|
B:PHE149
|
4.8
|
18.7
|
1.0
|
CZ
|
B:PHE149
|
4.8
|
22.0
|
1.0
|
OD2
|
B:ASP106
|
4.9
|
21.9
|
1.0
|
NE1
|
B:TRP107
|
5.0
|
18.5
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 7ziy
Go back to
Fluorine Binding Sites List in 7ziy
Fluorine binding site 6 out
of 6 in the X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of X-Ray Structure of the Haloalkane Dehalogenase HALOTAG7 Bound to A Pentyltrifluoromethanesulfonamide Tetramethylrhodamine Ligand (Tmr- T5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F302
b:25.0
occ:1.00
|
F2
|
B:IYI302
|
0.0
|
25.0
|
1.0
|
C10
|
B:IYI302
|
1.3
|
25.8
|
1.0
|
F
|
B:IYI302
|
2.1
|
26.2
|
1.0
|
F1
|
B:IYI302
|
2.2
|
26.8
|
1.0
|
S
|
B:IYI302
|
2.6
|
21.0
|
1.0
|
O3
|
B:IYI302
|
2.9
|
23.1
|
1.0
|
O4
|
B:IYI302
|
3.1
|
23.6
|
1.0
|
CB
|
B:LEU209
|
3.3
|
13.9
|
1.0
|
NE1
|
B:TRP107
|
3.3
|
18.5
|
1.0
|
CD1
|
B:LEU209
|
3.5
|
22.1
|
1.0
|
O
|
B:PHE205
|
3.6
|
16.2
|
1.0
|
CA
|
B:PRO206
|
3.7
|
16.4
|
1.0
|
CG
|
B:LEU209
|
3.7
|
16.8
|
1.0
|
N1
|
B:IYI302
|
3.8
|
24.0
|
1.0
|
CD2
|
B:LEU209
|
4.1
|
22.4
|
1.0
|
CA
|
B:LEU209
|
4.1
|
14.4
|
1.0
|
CE2
|
B:TRP107
|
4.1
|
15.7
|
1.0
|
C
|
B:PHE205
|
4.1
|
15.8
|
1.0
|
N
|
B:PRO206
|
4.1
|
16.3
|
1.0
|
CZ2
|
B:TRP107
|
4.2
|
15.6
|
1.0
|
CD1
|
B:TRP107
|
4.3
|
18.0
|
1.0
|
N
|
B:LEU209
|
4.5
|
15.9
|
1.0
|
CB
|
B:PRO206
|
4.5
|
14.6
|
1.0
|
O
|
B:PRO206
|
4.5
|
16.2
|
1.0
|
C
|
B:PRO206
|
4.5
|
13.2
|
1.0
|
C9
|
B:IYI302
|
4.6
|
27.2
|
1.0
|
CD1
|
B:ILE132
|
4.8
|
18.0
|
1.0
|
|
Reference:
J.Kompa,
J.Bruins,
M.Glogger,
J.Wilhelm,
M.S.Frei,
M.Tarnawski,
E.D’Este,
M.Heilemann,
J.Hiblot,
K.Johnsson.
Exchangeable Halotag Ligands For Super-Resolution Fluorescence Microscopy J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.2C11969
Page generated: Fri Aug 2 16:10:16 2024
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