Atomistry » Fluorine » PDB 5fd2-5g3j » 5g17
Atomistry »
  Fluorine »
    PDB 5fd2-5g3j »
      5g17 »

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

Go back to Fluorine Binding Sites List in 5g17
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: Thu Aug 1 09:31:33 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy