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:

Calcium (Ca) 2 atoms

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

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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 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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