Zinc in PDB 8d9b: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 9

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 9, PDB code: 8d9b 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)	59.14 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.783, 91.468, 96.627, 90, 90, 90
R / Rfree (%)	18.3 / 22

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 9 also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Fluorine	(F)	8 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 9 (pdb code 8d9b). 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 9, PDB code: 8d9b:
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 9


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 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:15.3 occ:1.00 OD1 A:ASP612 2.0 13.4 1.0 OD2 A:ASP705 2.0 13.9 1.0 O06 A:QI8801 2.1 21.0 1.0 ND1 A:HIS614 2.1 13.6 1.0 O07 A:QI8801 2.4 26.1 1.0 CG A:ASP612 2.7 12.5 1.0 OD2 A:ASP612 2.8 14.2 1.0 N05 A:QI8801 2.8 29.5 1.0 C04 A:QI8801 2.9 28.6 1.0 CE1 A:HIS614 3.0 18.3 1.0 CG A:ASP705 3.0 14.8 1.0 CG A:HIS614 3.2 15.7 1.0 OD1 A:ASP705 3.4 14.5 1.0 CB A:HIS614 3.6 14.7 1.0 N A:HIS614 3.9 13.5 1.0 NE2 A:HIS573 4.1 15.7 1.0 NE2 A:HIS614 4.2 16.5 1.0 CB A:ASP612 4.2 14.0 1.0 CG1 A:VAL613 4.3 13.8 1.0 CD2 A:HIS614 4.3 17.3 1.0 C03 A:QI8801 4.3 21.9 1.0 CB A:ASP705 4.3 13.5 1.0 CA A:GLY743 4.3 13.4 1.0 N A:VAL613 4.4 13.4 1.0 O A:HOH920 4.4 29.0 1.0 CA A:HIS614 4.4 13.8 1.0 F09 A:QI8801 4.4 24.3 1.0 OH A:TYR745 4.4 19.6 1.0 CE1 A:HIS573 4.5 13.2 1.0 CE2 A:TYR745 4.6 15.1 1.0 N A:GLY743 4.7 13.7 1.0 NE2 A:HIS574 4.7 16.5 1.0 C08 A:QI8801 4.9 27.4 1.0 C A:VAL613 4.9 15.6 1.0 C A:ASP612 4.9 12.1 1.0 CA A:ASP612 4.9 11.8 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 9


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 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:15.2 occ:1.00 OD2 B:ASP705 2.0 13.6 1.0 OD1 B:ASP612 2.0 13.6 1.0 O06 B:QI8801 2.1 20.3 1.0 ND1 B:HIS614 2.1 13.2 1.0 O07 B:QI8801 2.5 24.5 1.0 CG B:ASP612 2.7 12.9 1.0 OD2 B:ASP612 2.7 14.8 1.0 N05 B:QI8801 2.8 26.7 1.0 C04 B:QI8801 2.9 27.0 1.0 CE1 B:HIS614 3.0 14.4 1.0 CG B:ASP705 3.0 16.0 1.0 CG B:HIS614 3.2 14.5 1.0 OD1 B:ASP705 3.4 15.0 1.0 CB B:HIS614 3.6 14.8 1.0 N B:HIS614 3.9 11.3 1.0 NE2 B:HIS573 4.1 14.6 1.0 NE2 B:HIS614 4.2 16.1 1.0 CB B:ASP612 4.2 16.0 1.0 CG1 B:VAL613 4.2 12.6 1.0 CD2 B:HIS614 4.3 17.0 1.0 CB B:ASP705 4.3 12.2 1.0 C03 B:QI8801 4.3 19.8 1.0 N B:VAL613 4.4 13.0 1.0 CA B:GLY743 4.4 13.6 1.0 CA B:HIS614 4.4 14.8 1.0 OH B:TYR745 4.4 20.1 1.0 F09 B:QI8801 4.5 28.8 1.0 CE1 B:HIS573 4.5 13.3 1.0 O B:HOH987 4.6 26.6 1.0 CE2 B:TYR745 4.6 16.7 1.0 N B:GLY743 4.7 14.2 1.0 NE2 B:HIS574 4.8 16.7 1.0 C B:VAL613 4.9 13.6 1.0 C B:ASP612 4.9 13.2 1.0 C08 B:QI8801 4.9 23.8 1.0 CA B:ASP612 4.9 12.4 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