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Fluorine in PDB 5g17: Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.

Enzymatic activity of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.

All present enzymatic activity of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.:
3.5.1.4;

Protein crystallography data

The structure of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide., PDB code: 5g17 was solved by A.Kraemer, F.J.Meyer-Almes, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.68 / 1.51
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.270, 101.270, 175.220, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 15.8

Other elements in 5g17:

The structure of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. also contains other interesting chemical elements:

Potassium (K) 4 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. (pdb code 5g17). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide., PDB code: 5g17:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5g17

Go back to Fluorine Binding Sites List in 5g17
Fluorine binding site 1 out of 6 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:11.9
occ:1.00
F2 A:6DK373 0.0 11.9 1.0
C A:6DK373 1.3 10.9 1.0
F1 A:6DK373 2.1 12.4 1.0
F A:6DK373 2.2 13.5 1.0
C1 A:6DK373 2.3 10.0 1.0
O2 A:6DK373 2.9 9.2 1.0
C2 A:6DK373 2.9 12.5 1.0
CD2 A:HIS143 3.1 10.2 1.0
SG A:CYS153 3.2 9.6 1.0
O A:GLY151 3.3 12.2 1.0
CD2 A:HIS142 3.3 9.3 1.0
NE2 A:HIS142 3.4 9.5 1.0
NE2 A:HIS143 3.6 10.2 1.0
O1 A:6DK373 3.6 9.9 1.0
CG A:PRO140 3.8 8.4 1.0
CB A:PRO140 3.9 8.7 1.0
CG A:HIS143 4.1 9.4 1.0
C3 A:6DK373 4.3 14.7 1.0
C A:GLY151 4.5 12.4 1.0
ZN A:ZN370 4.6 8.8 0.5
CG A:HIS142 4.6 8.6 1.0
OE1 A:GLU309 4.6 9.4 1.0
OH A:TYR312 4.6 10.5 1.0
CE1 A:HIS143 4.7 9.5 1.0
CE1 A:HIS142 4.7 8.9 1.0
N A:HIS143 4.7 8.2 1.0
OD2 A:ASP180 4.8 7.4 1.0
N A:HIS142 4.8 8.9 1.0
CB A:HIS143 4.8 9.5 1.0
CB A:CYS153 4.9 9.4 1.0
N A:GLY141 5.0 7.9 1.0
ND1 A:HIS143 5.0 9.0 1.0

Fluorine binding site 2 out of 6 in 5g17

Go back to Fluorine Binding Sites List in 5g17
Fluorine binding site 2 out of 6 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:13.5
occ:1.00
F A:6DK373 0.0 13.5 1.0
C A:6DK373 1.3 10.9 1.0
F1 A:6DK373 2.2 12.4 1.0
F2 A:6DK373 2.2 11.9 1.0
C1 A:6DK373 2.3 10.0 1.0
O1 A:6DK373 2.8 9.9 1.0
OH A:TYR312 2.8 10.5 1.0
C2 A:6DK373 2.9 12.5 1.0
O A:HOH2103 3.1 12.8 1.0
CG A:PRO140 3.1 8.4 1.0
CB A:PRO140 3.5 8.7 1.0
O2 A:6DK373 3.6 9.2 1.0
CD2 A:PHE152 3.9 13.9 1.0
CA A:GLY310 3.9 8.0 1.0
O A:GLY151 3.9 12.2 1.0
CZ A:TYR312 4.1 9.1 1.0
N A:GLY310 4.2 8.0 1.0
C3 A:6DK373 4.3 14.7 1.0
CB A:PHE152 4.4 14.3 1.0
CD A:PRO140 4.5 7.9 1.0
ZN A:ZN370 4.5 8.8 0.5
CG A:PHE152 4.6 14.4 1.0
SG A:CYS153 4.6 9.6 1.0
C A:GLU309 4.7 8.2 1.0
OD2 A:ASP180 4.7 7.4 1.0
CE2 A:PHE152 4.8 15.4 1.0
O A:GLU309 4.9 8.7 1.0
CE2 A:TYR312 4.9 8.5 1.0
CD2 A:HIS143 4.9 10.2 1.0
CE1 A:TYR312 4.9 9.7 1.0
NE2 A:HIS142 5.0 9.5 1.0

Fluorine binding site 3 out of 6 in 5g17

Go back to Fluorine Binding Sites List in 5g17
Fluorine binding site 3 out of 6 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:12.4
occ:1.00
F1 A:6DK373 0.0 12.4 1.0
C A:6DK373 1.3 10.9 1.0
F2 A:6DK373 2.1 11.9 1.0
F A:6DK373 2.2 13.5 1.0
C1 A:6DK373 2.4 10.0 1.0
O2 A:6DK373 2.8 9.2 1.0
O1 A:6DK373 2.8 9.9 1.0
OD2 A:ASP180 3.0 7.4 1.0
N A:GLY310 3.0 8.0 1.0
NE2 A:HIS142 3.2 9.5 1.0
CA A:GLY310 3.4 8.0 1.0
CD2 A:HIS142 3.4 9.3 1.0
ZN A:ZN370 3.5 8.8 0.5
C A:GLU309 3.6 8.2 1.0
C2 A:6DK373 3.7 12.5 1.0
CB A:PRO140 3.7 8.7 1.0
CB A:GLU309 3.8 8.1 1.0
CG A:ASP180 3.8 7.0 1.0
OE1 A:GLU309 4.0 9.4 1.0
CA A:GLU309 4.0 7.9 1.0
OH A:TYR312 4.2 10.5 1.0
CG A:PRO140 4.2 8.4 1.0
OD1 A:ASP180 4.2 7.3 1.0
CE1 A:HIS142 4.3 8.9 1.0
O A:GLU309 4.4 8.7 1.0
O A:HOH2103 4.5 12.8 1.0
CG A:HIS142 4.6 8.6 1.0
NE2 A:HIS143 4.7 10.2 1.0
CD2 A:HIS143 4.7 10.2 1.0
CD A:GLU309 4.8 10.3 1.0
SG A:CYS153 4.8 9.6 1.0
OD2 A:ASP268 4.8 7.8 1.0
CB A:ASP180 4.8 7.6 1.0
CG A:GLU309 4.8 8.8 1.0
C A:GLY310 4.8 8.0 1.0
C3 A:6DK373 5.0 14.7 1.0

Fluorine binding site 4 out of 6 in 5g17

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Fluorine binding site 4 out of 6 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F373

b:13.7
occ:1.00
F2 B:6DK373 0.0 13.7 1.0
C B:6DK373 1.3 11.5 1.0
F1 B:6DK373 2.1 12.7 1.0
F B:6DK373 2.2 11.2 1.0
C1 B:6DK373 2.4 10.0 1.0
O2 B:6DK373 2.8 9.7 1.0
OH B:TYR312 2.8 11.0 1.0
C2 B:6DK373 2.9 12.1 1.0
CG B:PRO140 3.1 9.2 1.0
O B:HOH2111 3.1 14.6 1.0
CB B:PRO140 3.5 8.7 1.0
O1 B:6DK373 3.6 9.7 1.0
CA B:GLY310 3.9 8.8 1.0
CD2 B:PHE152 3.9 17.6 1.0
O B:GLY151 4.0 13.0 1.0
CZ B:TYR312 4.2 9.7 1.0
N B:GLY310 4.2 8.5 1.0
C3 B:6DK373 4.3 14.4 1.0
CB B:PHE152 4.4 15.3 1.0
CD B:PRO140 4.4 8.8 1.0
ZN B:ZN370 4.5 8.8 0.5
C B:GLU309 4.6 8.5 1.0
SG B:CYS153 4.6 9.4 1.0
CG B:PHE152 4.6 16.3 1.0
OD2 B:ASP180 4.7 8.6 1.0
CE2 B:PHE152 4.8 18.5 1.0
O B:GLU309 4.8 9.4 1.0
CA B:PRO140 4.9 8.1 1.0
NE2 B:HIS142 5.0 9.9 1.0
CD2 B:HIS143 5.0 9.1 1.0
CE2 B:TYR312 5.0 8.6 1.0
CE1 B:TYR312 5.0 10.4 1.0
NZ B:LYS43 5.0 9.8 1.0

Fluorine binding site 5 out of 6 in 5g17

Go back to Fluorine Binding Sites List in 5g17
Fluorine binding site 5 out of 6 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F373

b:11.2
occ:1.00
F B:6DK373 0.0 11.2 1.0
C B:6DK373 1.3 11.5 1.0
F1 B:6DK373 2.1 12.7 1.0
F2 B:6DK373 2.2 13.7 1.0
C1 B:6DK373 2.3 10.0 1.0
O1 B:6DK373 2.9 9.7 1.0
C2 B:6DK373 2.9 12.1 1.0
CD2 B:HIS143 3.1 9.1 1.0
SG B:CYS153 3.2 9.4 1.0
O B:GLY151 3.3 13.0 1.0
CD2 B:HIS142 3.3 9.3 1.0
NE2 B:HIS142 3.4 9.9 1.0
NE2 B:HIS143 3.5 9.5 1.0
O2 B:6DK373 3.6 9.7 1.0
CG B:PRO140 3.8 9.2 1.0
CB B:PRO140 3.9 8.7 1.0
CG B:HIS143 4.1 8.8 1.0
C3 B:6DK373 4.3 14.4 1.0
C B:GLY151 4.5 12.5 1.0
ZN B:ZN370 4.6 8.8 0.5
CG B:HIS142 4.6 8.4 1.0
OE1 B:GLU309 4.6 9.6 1.0
OH B:TYR312 4.6 11.0 1.0
CE1 B:HIS143 4.7 9.3 1.0
CE1 B:HIS142 4.7 9.6 1.0
N B:HIS143 4.8 8.3 1.0
N B:HIS142 4.8 8.7 1.0
OD2 B:ASP180 4.8 8.6 1.0
CB B:HIS143 4.8 8.9 1.0
CB B:CYS153 4.9 9.7 1.0
ND1 B:HIS143 4.9 8.8 1.0
N B:GLY141 5.0 7.9 1.0

Fluorine binding site 6 out of 6 in 5g17

Go back to Fluorine Binding Sites List in 5g17
Fluorine binding site 6 out of 6 in the Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Bordetella Alcaligenes Hdah (T101A) Bound to 9,9,9-Trifluoro-8,8- Dihydroxy-N-Phenylnonanamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F373

b:12.7
occ:1.00
F1 B:6DK373 0.0 12.7 1.0
C B:6DK373 1.3 11.5 1.0
F B:6DK373 2.1 11.2 1.0
F2 B:6DK373 2.1 13.7 1.0
C1 B:6DK373 2.3 10.0 1.0
O1 B:6DK373 2.7 9.7 1.0
O2 B:6DK373 2.7 9.7 1.0
OD2 B:ASP180 3.0 8.6 1.0
N B:GLY310 3.0 8.5 1.0
NE2 B:HIS142 3.2 9.9 1.0
CA B:GLY310 3.4 8.8 1.0
CD2 B:HIS142 3.4 9.3 1.0
ZN B:ZN370 3.5 8.8 0.5
C B:GLU309 3.6 8.5 1.0
C2 B:6DK373 3.7 12.1 1.0
CB B:PRO140 3.7 8.7 1.0
CB B:GLU309 3.8 8.3 1.0
CG B:ASP180 3.9 7.4 1.0
OE1 B:GLU309 4.0 9.6 1.0
CA B:GLU309 4.0 8.3 1.0
OH B:TYR312 4.2 11.0 1.0
CG B:PRO140 4.2 9.2 1.0
OD1 B:ASP180 4.3 8.0 1.0
CE1 B:HIS142 4.3 9.6 1.0
O B:GLU309 4.4 9.4 1.0
O B:HOH2111 4.6 14.6 1.0
CG B:HIS142 4.6 8.4 1.0
NE2 B:HIS143 4.7 9.5 1.0
CD2 B:HIS143 4.7 9.1 1.0
C B:GLY310 4.8 8.8 1.0
CD B:GLU309 4.8 9.8 1.0
OD2 B:ASP268 4.8 7.9 1.0
SG B:CYS153 4.8 9.4 1.0
CB B:ASP180 4.9 7.7 1.0
CG B:GLU309 4.9 9.5 1.0
C3 B:6DK373 5.0 14.4 1.0

Reference:

C.Meyners, A.Kramer, O.Yildiz, F.J.Meyer-Almes. The Thermodynamic Signature of Ligand Binding to Histone Deacetylase-Like Amidohydrolases Is Most Sensitive to the Flexibility in the L2-Loop Lining the Active Site Pocket. Biochim. Biophys. Acta V.1861 1855 2017.
ISSN: ISSN 0006-3002
PubMed: 28389333
DOI: 10.1016/J.BBAGEN.2017.04.001
Page generated: Sun Dec 13 12:22:51 2020

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