Fluorine in PDB 8d98: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5, PDB code: 8d98 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)	59.28 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.923, 91.468, 96.92, 90, 90, 90
R / Rfree (%)	18.3 / 21.1

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5 also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5 (pdb code 8d98). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5, PDB code: 8d98:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:30.0 occ:1.00 F01 A:QHX801 0.0 30.0 1.0 C02 A:QHX801 1.4 23.4 1.0 C03 A:QHX801 2.4 27.3 1.0 C12 A:QHX801 2.4 24.1 1.0 CZ A:PHE643 3.0 23.0 1.0 CB A:SER531 3.1 21.4 1.0 CE1 A:PHE643 3.3 21.9 1.0 CA A:GLY582 3.3 13.7 1.0 CE2 A:PHE643 3.4 20.8 1.0 OG A:SER531 3.5 23.8 1.0 C04 A:QHX801 3.6 30.9 1.0 C07 A:QHX801 3.6 26.6 1.0 CD1 A:PHE643 3.9 23.0 1.0 CE1 A:PHE583 3.9 20.0 1.0 CD2 A:PHE643 3.9 20.8 1.0 C A:GLY582 4.0 13.8 1.0 CZ A:PHE583 4.1 19.1 1.0 C06 A:QHX801 4.1 28.4 1.0 CG A:PHE643 4.1 19.4 1.0 CD1 A:PHE583 4.2 17.5 1.0 N A:GLY582 4.4 16.6 1.0 O A:SER531 4.4 16.5 1.0 O A:GLY582 4.4 13.7 1.0 CA A:SER531 4.6 17.2 1.0 N A:PHE583 4.7 12.4 1.0 CE2 A:PHE583 4.7 17.8 1.0 F05 A:QHX801 4.7 42.9 1.0 CG A:PHE583 4.8 15.7 1.0 C08 A:QHX801 4.9 32.2 1.0 C A:SER531 5.0 19.4 1.0 CD2 A:PHE583 5.0 18.0 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:42.9 occ:1.00 F05 A:QHX801 0.0 42.9 1.0 C04 A:QHX801 1.4 30.9 1.0 C06 A:QHX801 2.4 28.4 1.0 C03 A:QHX801 2.4 27.3 1.0 CD1 A:LEU712 3.4 26.6 1.0 C07 A:QHX801 3.6 26.6 1.0 C02 A:QHX801 3.6 23.4 1.0 CD2 A:LEU712 3.8 24.7 1.0 CG A:LEU712 4.0 18.3 1.0 C12 A:QHX801 4.1 24.1 1.0 NE2 A:HIS614 4.2 18.9 1.0 CB A:LEU712 4.3 17.4 1.0 CE1 A:HIS614 4.4 17.2 1.0 CZ A:PHE583 4.5 19.1 1.0 CE2 A:PHE583 4.7 17.8 1.0 F01 A:QHX801 4.7 30.0 1.0 C08 A:QHX801 4.8 32.2 1.0 N09 A:QHX801 5.0 26.4 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:38.2 occ:1.00 F01 B:QHX801 0.0 38.2 1.0 C02 B:QHX801 1.4 31.2 1.0 C12 B:QHX801 2.4 26.6 1.0 C03 B:QHX801 2.4 25.4 1.0 O B:HOH985 3.1 22.8 1.0 CD1 B:LEU712 3.5 22.1 1.0 C07 B:QHX801 3.6 23.8 1.0 C04 B:QHX801 3.6 22.7 1.0 CD2 B:LEU712 3.8 18.7 1.0 CG B:LEU712 4.0 22.5 1.0 C06 B:QHX801 4.1 23.5 1.0 NE2 B:HIS614 4.1 13.9 1.0 CB B:LEU712 4.2 16.5 1.0 CE1 B:HIS614 4.3 16.1 1.0 CZ B:PHE583 4.7 17.7 1.0 F05 B:QHX801 4.7 27.3 1.0 C08 B:QHX801 4.8 30.0 1.0 CE2 B:PHE583 4.9 19.5 1.0 N09 B:QHX801 5.0 27.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:27.3 occ:1.00 F05 B:QHX801 0.0 27.3 1.0 C04 B:QHX801 1.4 22.7 1.0 C03 B:QHX801 2.4 25.4 1.0 C06 B:QHX801 2.4 23.5 1.0 CZ B:PHE643 3.0 19.3 1.0 CB B:SER531 3.1 21.7 1.0 OG B:SER531 3.3 18.6 1.0 CE1 B:PHE643 3.3 15.8 1.0 CA B:GLY582 3.4 14.5 1.0 CE2 B:PHE643 3.4 17.4 1.0 C02 B:QHX801 3.6 31.2 1.0 C07 B:QHX801 3.6 23.8 1.0 CE1 B:PHE583 3.8 18.1 1.0 CD1 B:PHE643 4.0 17.1 1.0 CD2 B:PHE643 4.0 15.3 1.0 C B:GLY582 4.1 15.0 1.0 CZ B:PHE583 4.1 17.7 1.0 C12 B:QHX801 4.1 26.6 1.0 CD1 B:PHE583 4.2 15.6 1.0 CG B:PHE643 4.3 14.9 1.0 O B:SER531 4.4 17.2 1.0 N B:GLY582 4.4 12.3 1.0 O B:GLY582 4.5 14.8 1.0 CA B:SER531 4.5 16.9 1.0 N B:PHE583 4.7 12.8 1.0 CE2 B:PHE583 4.7 19.5 1.0 F01 B:QHX801 4.7 38.2 1.0 CG B:PHE583 4.8 16.6 1.0 C08 B:QHX801 4.9 30.0 1.0 C B:SER531 5.0 17.9 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