Fluorine in PDB 8d99: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7, PDB code: 8d99 was solved by P.R.Watson, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.25 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.9, 95.576, 96.852, 90, 90, 90
R / Rfree (%)	19.1 / 22

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7 also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7 (pdb code 8d99). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7, PDB code: 8d99:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:26.1 occ:0.57 F01 B:QH7801 0.0 26.1 0.6 C02 B:QH7801 1.4 24.2 0.6 C03 B:QH7801 2.4 23.2 0.6 C13 B:QH7801 2.4 22.5 0.6 N05 B:QH7801 2.6 25.5 0.6 CE1 B:HIS614 2.9 15.8 1.0 C04 B:QH7801 2.9 29.1 0.6 CD1 B:LEU712 3.1 21.7 1.0 CE2 B:TYR745 3.2 18.0 1.0 NE2 B:HIS614 3.4 18.1 1.0 C08 B:QH7801 3.6 24.1 0.6 C12 B:QH7801 3.6 24.7 0.6 O B:HOH926 3.7 28.5 1.0 CB B:LEU712 3.8 19.0 1.0 ND1 B:HIS614 3.8 19.1 1.0 O06 B:QH7801 3.9 27.6 0.6 CZ B:TYR745 3.9 19.2 1.0 CD2 B:TYR745 3.9 16.1 1.0 OH B:TYR745 4.0 20.1 1.0 CG B:LEU712 4.0 24.9 1.0 O07 B:QH7801 4.0 29.7 0.6 C10 B:QH7801 4.1 21.5 0.6 OD2 B:ASP705 4.2 15.5 1.0 CE2 B:PHE583 4.3 21.8 1.0 ZN B:ZN802 4.4 20.8 1.0 CD2 B:HIS614 4.5 16.3 1.0 F09 B:QH7801 4.7 26.1 0.6 CG B:HIS614 4.8 16.0 1.0 CD2 B:LEU712 4.8 20.8 1.0 CZ B:PHE583 5.0 20.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:26.1 occ:0.57 F09 B:QH7801 0.0 26.1 0.6 C08 B:QH7801 1.4 24.1 0.6 C03 B:QH7801 2.3 23.2 0.6 C10 B:QH7801 2.4 21.5 0.6 O07 B:QH7801 2.4 29.7 0.6 C04 B:QH7801 2.7 29.1 0.6 F11 B:QH7801 2.8 29.8 0.6 O B:GLY582 2.8 15.7 1.0 CA B:GLY582 3.0 14.3 1.0 C B:GLY582 3.1 17.1 1.0 CE1 B:PHE643 3.3 18.5 1.0 CD2 B:HIS574 3.4 16.1 1.0 C02 B:QH7801 3.6 24.2 0.6 NE2 B:HIS574 3.6 17.8 1.0 C12 B:QH7801 3.7 24.7 0.6 CZ B:PHE643 3.8 18.7 1.0 CD2 B:PHE583 3.8 20.6 1.0 CD1 B:PHE643 3.9 18.3 1.0 CE2 B:PHE583 4.0 21.8 1.0 CG B:PHE583 4.1 16.9 1.0 C13 B:QH7801 4.1 22.5 0.6 N B:PHE583 4.2 13.1 1.0 N05 B:QH7801 4.2 25.5 0.6 CZ B:PHE583 4.3 20.4 1.0 CD1 B:PHE583 4.4 14.6 1.0 N B:GLY582 4.4 13.0 1.0 CE1 B:PHE583 4.5 17.5 1.0 CG B:HIS574 4.5 15.2 1.0 O B:HOH901 4.6 23.9 1.0 CE2 B:PHE643 4.7 17.2 1.0 CB B:PHE583 4.7 12.4 1.0 F01 B:QH7801 4.7 26.1 0.6 CE1 B:HIS574 4.7 18.6 1.0 CG B:PHE643 4.8 18.1 1.0 CB B:SER531 5.0 23.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:29.8 occ:0.57 F11 B:QH7801 0.0 29.8 0.6 C10 B:QH7801 1.4 21.5 0.6 C12 B:QH7801 2.4 24.7 0.6 C08 B:QH7801 2.4 24.1 0.6 F09 B:QH7801 2.8 26.1 0.6 CZ B:PHE643 3.0 18.7 1.0 CE2 B:PHE643 3.1 17.2 1.0 CB B:SER531 3.1 23.7 1.0 OG B:SER531 3.1 25.4 1.0 CE1 B:PHE643 3.4 18.5 1.0 CD2 B:PHE643 3.5 16.4 1.0 C03 B:QH7801 3.6 23.2 0.6 C13 B:QH7801 3.6 22.5 0.6 CD1 B:PHE643 3.8 18.3 1.0 CG B:PHE643 3.8 18.1 1.0 CA B:GLY582 3.8 14.3 1.0 C02 B:QH7801 4.1 24.2 0.6 CZ B:PHE583 4.2 20.4 1.0 CE1 B:PHE583 4.2 17.5 1.0 C B:GLY582 4.6 17.1 1.0 CA B:SER531 4.6 20.9 1.0 CE2 B:PHE583 4.7 21.8 1.0 CD1 B:PHE583 4.8 14.6 1.0 O B:SER531 4.8 16.8 1.0 N B:GLY582 4.8 13.0 1.0 C04 B:QH7801 4.9 29.1 0.6 OD1 B:ASN530 4.9 24.6 1.0 CB B:PHE643 4.9 14.4 1.0 O B:GLY582 5.0 15.7 1.0

P.R.Watson, P.Bai, C.Wang, A.D.Cragin, J.M.Hooker, D.W.Christianson. Aromatic Ring Fluorination Patterns Modulate Inhibitory Potency of Fluorophenylhydroxamates Complexed with Histone Deacetylase 6. Biochemistry V. 61 1945 2022.
ISSN: ISSN 0006-2960
PubMed: 36073962
DOI: 10.1021/ACS.BIOCHEM.2C00332