Zinc in PDB 8d9a: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8, PDB code: 8d9a 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)	66.51 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.035, 92.044, 96.2, 90, 90, 90
R / Rfree (%)	18.3 / 21.7

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8 also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Fluorine	(F)	6 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8 (pdb code 8d9a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8, PDB code: 8d9a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:17.5 occ:1.00 OD1 A:ASP612 2.0 11.8 1.0 OD2 A:ASP705 2.0 14.2 1.0 O06 A:QHO801 2.1 18.0 1.0 ND1 A:HIS614 2.1 15.3 1.0 O07 A:QHO801 2.6 32.6 1.0 N05 A:QHO801 2.6 29.9 1.0 CG A:ASP612 2.7 13.8 1.0 OD2 A:ASP612 2.7 14.4 1.0 C04 A:QHO801 2.9 31.0 1.0 CE1 A:HIS614 3.0 12.3 1.0 CG A:ASP705 3.0 14.0 1.0 CG A:HIS614 3.2 16.8 1.0 OD1 A:ASP705 3.4 13.8 1.0 CB A:HIS614 3.6 14.3 1.0 N A:HIS614 3.9 13.6 1.0 NE2 A:HIS573 4.1 14.2 1.0 NE2 A:HIS614 4.1 18.5 1.0 CB A:ASP612 4.2 16.1 1.0 C03 A:QHO801 4.3 26.4 1.0 CD2 A:HIS614 4.3 15.9 1.0 CG1 A:VAL613 4.3 10.6 1.0 CA A:GLY743 4.3 9.0 1.0 CB A:ASP705 4.3 10.7 1.0 N A:VAL613 4.3 12.6 1.0 OH A:TYR745 4.4 19.8 1.0 CA A:HIS614 4.4 14.1 1.0 CE1 A:HIS573 4.4 13.6 1.0 CE2 A:TYR745 4.6 18.6 1.0 N A:GLY743 4.7 14.7 1.0 NE2 A:HIS574 4.7 15.5 1.0 C08 A:QHO801 4.8 25.3 1.0 C A:ASP612 4.9 16.3 1.0 C A:VAL613 4.9 14.8 1.0 CA A:ASP612 4.9 13.1 1.0 CZ A:TYR745 5.0 20.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:17.7 occ:1.00 OD1 B:ASP612 2.0 11.4 1.0 OD2 B:ASP705 2.0 13.1 1.0 O06 B:QHO801 2.0 18.3 1.0 ND1 B:HIS614 2.1 11.4 1.0 O07 B:QHO801 2.6 30.7 1.0 N05 B:QHO801 2.6 28.8 1.0 CG B:ASP612 2.7 13.7 1.0 OD2 B:ASP612 2.7 12.3 1.0 C04 B:QHO801 2.9 30.0 1.0 CE1 B:HIS614 3.0 17.0 1.0 CG B:ASP705 3.0 12.2 1.0 CG B:HIS614 3.2 18.3 1.0 OD1 B:ASP705 3.4 11.6 1.0 CB B:HIS614 3.6 16.4 1.0 N B:HIS614 3.9 13.0 1.0 NE2 B:HIS573 4.1 12.5 1.0 CB B:ASP612 4.2 13.6 1.0 NE2 B:HIS614 4.2 15.4 1.0 C03 B:QHO801 4.2 25.4 1.0 CA B:GLY743 4.3 10.4 1.0 CD2 B:HIS614 4.3 15.4 1.0 CG1 B:VAL613 4.3 11.4 1.0 N B:VAL613 4.3 11.3 1.0 CB B:ASP705 4.3 12.7 1.0 OH B:TYR745 4.4 20.8 1.0 CA B:HIS614 4.4 11.0 1.0 CE1 B:HIS573 4.5 10.8 1.0 CE2 B:TYR745 4.6 16.7 1.0 NE2 B:HIS574 4.6 15.8 1.0 N B:GLY743 4.7 12.2 1.0 C08 B:QHO801 4.8 29.7 1.0 C B:ASP612 4.9 12.6 1.0 C B:VAL613 4.9 16.3 1.0 CA B:ASP612 4.9 10.2 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