Zinc in PDB 5eem: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2

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

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2, PDB code: 5eem 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)	15.91 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.485, 55.400, 74.183, 73.58, 89.84, 82.64
R / Rfree (%)	22.4 / 27.3

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

Potassium	(K)	4 atoms
Sodium	(Na)	1 atom

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:28.8 occ:1.00 OD2 B:ASP705 1.9 14.0 1.0 OD1 B:ASP612 2.2 9.9 1.0 ND1 B:HIS614 2.2 8.6 1.0 O1 B:FMT805 2.2 38.7 1.0 O2 B:FMT805 2.4 34.0 1.0 C B:FMT805 2.6 17.7 1.0 OD2 B:ASP612 2.8 9.2 1.0 CG B:ASP612 2.8 10.9 1.0 CE1 B:HIS614 3.0 9.3 1.0 CG B:ASP705 3.0 13.8 1.0 CG B:HIS614 3.3 8.6 1.0 OD1 B:ASP705 3.6 14.4 1.0 CB B:HIS614 3.7 9.3 1.0 N B:HIS614 3.9 8.9 1.0 CA B:GLY743 4.2 12.1 1.0 CG1 B:VAL613 4.2 10.3 1.0 NE2 B:HIS614 4.2 8.3 1.0 NE2 B:HIS573 4.3 13.5 1.0 CB B:ASP705 4.3 13.9 1.0 N B:VAL613 4.3 11.8 1.0 CB B:ASP612 4.3 8.5 1.0 CD2 B:HIS614 4.3 8.1 1.0 OH B:TYR745 4.4 10.8 1.0 CA B:HIS614 4.4 10.1 1.0 CE1 B:HIS573 4.4 15.3 1.0 CE2 B:TYR745 4.6 13.8 1.0 N B:GLY743 4.6 12.8 1.0 NE2 B:HIS574 4.7 15.4 1.0 C B:VAL613 4.9 10.0 1.0 C B:ASP612 4.9 12.1 1.0 CZ B:TYR745 5.0 12.7 1.0 CA B:VAL613 5.0 11.5 1.0 C B:GLY743 5.0 12.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:30.6 occ:1.00 OD2 A:ASP705 1.9 10.3 1.0 ND1 A:HIS614 2.2 10.3 1.0 OD1 A:ASP612 2.3 9.9 1.0 O A:HOH926 2.3 30.4 1.0 OD2 A:ASP612 2.8 11.0 1.0 CG A:ASP612 2.8 12.3 1.0 CG A:ASP705 3.0 11.7 1.0 CE1 A:HIS614 3.1 9.8 1.0 CG A:HIS614 3.3 10.0 1.0 OD1 A:ASP705 3.6 11.6 1.0 CB A:HIS614 3.7 10.7 1.0 N A:HIS614 3.9 8.1 1.0 CA A:GLY743 4.1 9.7 1.0 NE2 A:HIS614 4.2 9.9 1.0 NE2 A:HIS573 4.2 9.5 1.0 CB A:ASP705 4.3 11.9 1.0 CG1 A:VAL613 4.3 13.5 1.0 CB A:ASP612 4.3 10.3 1.0 CD2 A:HIS614 4.3 10.7 1.0 OH A:TYR745 4.4 13.4 1.0 N A:VAL613 4.4 12.7 1.0 CA A:HIS614 4.4 9.3 1.0 CE1 A:HIS573 4.5 10.5 1.0 N A:GLY743 4.6 9.3 1.0 NE2 A:HIS574 4.6 14.9 1.0 CE2 A:TYR745 4.7 14.0 1.0 C A:GLY743 4.9 9.7 1.0 C A:ASP612 4.9 12.2 1.0 C A:VAL613 4.9 9.3 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