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

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

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha, PDB code: 5eei 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)	36.26 / 1.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.790, 83.551, 86.806, 90.00, 98.09, 90.00
R / Rfree (%)	12.5 / 14.8

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

Magnesium	(Mg)	2 atoms
Potassium	(K)	4 atoms
Chlorine	(Cl)	5 atoms

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


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 Saha within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:15.1 occ:0.79 OD2 A:ASP705 2.0 11.9 1.0 OD1 A:ASP612 2.0 12.2 1.0 O1 A:SHH2004 2.1 16.6 1.0 ND1 A:HIS614 2.1 12.3 1.0 O2 A:SHH2004 2.2 17.6 1.0 OD2 A:ASP612 2.6 12.3 1.0 CG A:ASP612 2.7 11.4 1.0 N1 A:SHH2004 2.7 18.4 1.0 C1 A:SHH2004 2.8 19.1 1.0 HO1 A:SHH2004 2.8 19.9 1.0 CG A:ASP705 3.0 12.3 1.0 CE1 A:HIS614 3.0 11.8 1.0 HE1 A:HIS614 3.1 14.2 1.0 HB2 A:HIS614 3.1 13.6 1.0 H A:HIS614 3.2 13.6 1.0 CG A:HIS614 3.2 11.5 1.0 HA3 A:GLY743 3.3 16.3 1.0 OD1 A:ASP705 3.3 12.7 1.0 HG11 A:VAL613 3.5 13.8 1.0 CB A:HIS614 3.7 11.3 1.0 HH A:TYR745 3.7 18.7 1.0 HE2 A:TYR745 3.8 17.6 1.0 H A:VAL613 3.9 13.1 1.0 N A:HIS614 3.9 11.3 1.0 H A:GLY743 4.0 14.9 1.0 HG13 A:VAL613 4.1 13.8 1.0 CB A:ASP612 4.2 11.1 1.0 C2 A:SHH2004 4.2 23.0 1.0 NE2 A:HIS614 4.2 11.9 1.0 CA A:GLY743 4.2 13.6 1.0 CG1 A:VAL613 4.3 11.5 1.0 NE2 A:HIS573 4.3 14.2 1.0 CB A:ASP705 4.3 12.3 1.0 CD2 A:HIS614 4.3 11.7 1.0 HE1 A:HIS573 4.3 16.9 1.0 N A:VAL613 4.3 10.9 1.0 H21 A:SHH2004 4.4 27.6 1.0 CA A:HIS614 4.4 10.9 1.0 HB3 A:HIS614 4.5 13.6 1.0 HB2 A:ASP705 4.5 14.7 1.0 HB3 A:ASP705 4.5 14.7 1.0 HB3 A:ASP612 4.5 13.3 1.0 OH A:TYR745 4.5 15.6 1.0 N A:GLY743 4.5 12.4 1.0 H A:GLY744 4.5 18.2 1.0 H32 A:SHH2004 4.6 29.8 1.0 CE2 A:TYR745 4.6 14.6 1.0 CE1 A:HIS573 4.7 14.1 1.0 HB2 A:ASP612 4.7 13.3 1.0 HA2 A:GLY743 4.7 16.3 1.0 HA3 A:GLY703 4.8 17.3 1.0 HA A:ASP612 4.8 13.1 1.0 C A:ASP612 4.8 11.5 1.0 CA A:ASP612 4.9 10.9 1.0 H22 A:SHH2004 4.9 27.6 1.0 C A:VAL613 4.9 11.7 1.0 HG12 A:VAL613 4.9 13.8 1.0 C3 A:SHH2004 4.9 24.8 1.0 C A:GLY743 4.9 15.1 1.0 N A:GLY744 5.0 15.2 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 Saha


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 Saha within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:15.4 occ:0.76 OD2 B:ASP705 2.0 13.9 1.0 O1 B:SHH801 2.0 17.6 1.0 OD1 B:ASP612 2.1 12.7 1.0 ND1 B:HIS614 2.2 13.1 1.0 O2 B:SHH801 2.2 19.0 1.0 OD2 B:ASP612 2.6 13.3 1.0 CG B:ASP612 2.7 13.0 1.0 HO1 B:SHH801 2.7 21.1 1.0 N1 B:SHH801 2.8 18.4 1.0 C1 B:SHH801 2.8 19.6 1.0 CG B:ASP705 3.0 13.5 1.0 CE1 B:HIS614 3.0 13.9 1.0 HB2 B:HIS614 3.1 15.9 1.0 HE1 B:HIS614 3.1 16.7 1.0 H B:HIS614 3.2 16.1 1.0 CG B:HIS614 3.2 13.1 1.0 HA3 B:GLY743 3.2 17.1 1.0 OD1 B:ASP705 3.3 13.6 1.0 HG12 B:VAL613 3.5 16.7 1.0 CB B:HIS614 3.6 13.2 1.0 HE2 B:TYR745 3.8 17.5 1.0 H B:GLY743 3.9 17.0 1.0 N B:HIS614 3.9 13.4 1.0 H B:VAL613 3.9 16.1 1.0 CB B:ASP612 4.1 13.4 1.0 CA B:GLY743 4.1 14.2 1.0 NE2 B:HIS614 4.2 14.0 1.0 C2 B:SHH801 4.2 22.4 1.0 NE2 B:HIS573 4.2 14.6 1.0 CB B:ASP705 4.3 13.8 1.0 CD2 B:HIS614 4.3 13.8 1.0 CG1 B:VAL613 4.3 13.9 1.0 HE1 B:HIS573 4.3 15.4 1.0 HG13 B:VAL613 4.3 16.7 1.0 N B:VAL613 4.4 13.4 1.0 HB3 B:HIS614 4.4 15.9 1.0 CA B:HIS614 4.4 13.1 1.0 N B:GLY743 4.4 14.1 1.0 HB3 B:ASP612 4.5 16.0 1.0 HB3 B:ASP705 4.5 16.6 1.0 HB2 B:ASP705 4.5 16.6 1.0 H31 B:SHH801 4.5 31.4 1.0 H22 B:SHH801 4.5 26.9 1.0 OH B:TYR745 4.5 15.4 1.0 H B:GLY744 4.5 18.7 1.0 CE2 B:TYR745 4.6 14.6 1.0 HB2 B:ASP612 4.6 16.0 1.0 CE1 B:HIS573 4.6 12.9 1.0 HA3 B:GLY703 4.7 17.1 1.0 HA2 B:GLY743 4.7 17.1 1.0 HA B:ASP612 4.8 15.2 1.0 C B:ASP612 4.8 13.0 1.0 CA B:ASP612 4.8 12.6 1.0 C3 B:SHH801 4.9 26.2 1.0 HG11 B:VAL613 4.9 16.7 1.0 C B:GLY743 4.9 15.4 1.0 C B:VAL613 4.9 13.5 1.0 H21 B:SHH801 4.9 26.9 1.0 N B:GLY744 5.0 15.6 1.0 NE2 B:HIS574 5.0 15.4 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