Zinc in PDB 5ef7: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob:
3.5.1.98;

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob, PDB code: 5ef7 was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.55 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.672, 56.637, 74.784, 106.45, 90.11, 97.09
R / Rfree (%)	18.1 / 22.1

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob (pdb code 5ef7). 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 in Complex with Hpob, PDB code: 5ef7:
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 in Complex with Hpob


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 in Complex with Hpob within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:15.4 occ:0.65 O2 A:5OJ804 1.9 46.6 1.0 OD2 A:ASP705 2.0 15.0 1.0 OD1 A:ASP612 2.1 11.3 1.0 O A:HOH921 2.1 24.1 1.0 ND1 A:HIS614 2.2 12.6 1.0 N1 A:5OJ804 2.4 45.9 1.0 CG A:ASP612 2.7 17.4 1.0 OD2 A:ASP612 2.8 16.0 1.0 CE1 A:HIS614 3.1 13.5 1.0 CG A:ASP705 3.1 17.0 1.0 CG A:HIS614 3.2 11.3 1.0 C1 A:5OJ804 3.3 43.9 1.0 O1 A:5OJ804 3.6 44.7 1.0 OD1 A:ASP705 3.6 18.7 1.0 CB A:HIS614 3.6 7.9 1.0 N A:HIS614 3.8 8.2 1.0 NE2 A:HIS573 4.1 14.8 1.0 NE2 A:HIS614 4.2 12.9 1.0 CB A:ASP612 4.2 13.5 1.0 CG1 A:VAL613 4.3 13.4 1.0 CD2 A:HIS614 4.3 13.4 1.0 N A:VAL613 4.3 12.2 1.0 CA A:HIS614 4.4 7.8 1.0 CB A:ASP705 4.4 12.0 1.0 C2 A:5OJ804 4.4 37.0 1.0 OH A:TYR745 4.4 21.0 1.0 NE2 A:HIS574 4.4 14.9 1.0 CE1 A:HIS573 4.5 17.6 1.0 CA A:GLY743 4.5 15.9 1.0 C A:VAL613 4.8 13.7 1.0 CE2 A:TYR745 4.8 18.0 1.0 C A:ASP612 4.9 15.2 1.0 N A:GLY743 4.9 14.3 1.0 C17 A:5OJ804 4.9 35.3 1.0 CA A:ASP612 5.0 16.0 1.0 CA A:VAL613 5.0 7.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob


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 in Complex with Hpob within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:17.5 occ:0.71 O2 B:5OJ804 2.0 48.0 1.0 O B:HOH905 2.0 29.0 1.0 OD2 B:ASP705 2.0 15.1 1.0 OD1 B:ASP612 2.1 14.8 1.0 ND1 B:HIS614 2.2 6.8 1.0 N1 B:5OJ804 2.5 47.4 1.0 CG B:ASP612 2.8 18.4 1.0 OD2 B:ASP612 2.8 18.9 1.0 CG B:ASP705 3.1 19.1 1.0 CE1 B:HIS614 3.1 7.7 1.0 CG B:HIS614 3.2 7.5 1.0 C1 B:5OJ804 3.3 45.9 1.0 OD1 B:ASP705 3.5 16.2 1.0 CB B:HIS614 3.5 6.8 1.0 O1 B:5OJ804 3.5 47.1 1.0 N B:HIS614 3.9 9.8 1.0 NE2 B:HIS573 4.1 12.3 1.0 NE2 B:HIS614 4.3 5.3 1.0 CB B:ASP612 4.3 13.6 1.0 CD2 B:HIS614 4.3 5.3 1.0 CA B:HIS614 4.3 14.0 1.0 CG1 B:VAL613 4.3 10.7 1.0 N B:VAL613 4.4 12.6 1.0 CB B:ASP705 4.4 17.0 1.0 CA B:GLY743 4.4 17.8 1.0 C2 B:5OJ804 4.4 40.2 1.0 CE1 B:HIS573 4.4 14.2 1.0 NE2 B:HIS574 4.5 16.1 1.0 OH B:TYR745 4.7 18.8 1.0 N B:GLY743 4.8 18.2 1.0 C B:VAL613 4.9 11.3 1.0 CE2 B:TYR745 4.9 22.2 1.0 C B:ASP612 4.9 13.7 1.0 C17 B:5OJ804 4.9 38.4 1.0 CA B:ASP612 5.0 13.1 1.0

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134