Zinc in PDB 4a69: Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate

All present enzymatic activity of Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate:
3.5.1.98;

The structure of Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate, PDB code: 4a69 was solved by P.J.Watson, L.Fairall, G.M.Santos, J.W.R.Schwabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.35 / 2.06
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	86.447, 118.634, 190.707, 90.00, 90.00, 90.00
R / Rfree (%)	18.702 / 23.617

The structure of Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate (pdb code 4a69). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate, PDB code: 4a69:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:17.8 occ:1.00 OD1 A:ASP170 1.9 18.3 1.0 OD2 A:ASP259 2.0 18.8 1.0 ND1 A:HIS172 2.0 17.2 1.0 OXT A:ACT501 2.1 24.0 1.0 O A:ACT501 2.5 25.4 1.0 C A:ACT501 2.6 25.0 1.0 CG A:ASP170 2.7 18.9 1.0 CE1 A:HIS172 2.9 17.6 1.0 OD2 A:ASP170 2.9 19.1 1.0 CG A:ASP259 3.0 18.4 1.0 CG A:HIS172 3.1 17.3 1.0 OD1 A:ASP259 3.3 18.2 1.0 CB A:HIS172 3.5 16.8 1.0 N A:HIS172 3.9 16.9 1.0 NE2 A:HIS172 4.1 16.7 1.0 CH3 A:ACT501 4.1 24.0 1.0 CA A:GLY296 4.1 18.9 1.0 CB A:ASP170 4.1 18.8 1.0 CD2 A:HIS172 4.2 16.9 1.0 CG2 A:ILE171 4.2 16.7 1.0 CB A:ASP259 4.3 18.6 1.0 N A:ILE171 4.3 18.8 1.0 CA A:HIS172 4.3 16.8 1.0 NE2 A:HIS134 4.4 19.7 1.0 CE2 A:TYR298 4.4 18.8 1.0 OH A:TYR298 4.5 20.1 1.0 N A:GLY296 4.6 18.9 1.0 NE2 A:HIS135 4.8 20.1 1.0 C A:ASP170 4.8 18.9 1.0 CA A:ASP170 4.8 18.9 1.0 C A:ILE171 4.8 17.6 1.0 CE1 A:HIS134 4.9 19.5 1.0 CE D:MET412 4.9 32.0 1.0 SD D:MET412 4.9 39.7 1.0 CA A:ILE171 5.0 17.5 1.0 CZ A:TYR298 5.0 18.9 1.0

Zinc binding site 2 out of 2 in the Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of HDAC3 Bound to Corepressor and Inositol Tetraphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:20.2 occ:1.00 OD2 B:ASP259 1.9 17.9 1.0 OD1 B:ASP170 1.9 18.1 1.0 ND1 B:HIS172 2.1 18.3 1.0 O B:ACT501 2.2 22.5 1.0 OXT B:ACT501 2.5 23.1 1.0 C B:ACT501 2.7 22.6 1.0 CG B:ASP170 2.8 19.9 1.0 CE1 B:HIS172 3.0 18.2 1.0 CG B:ASP259 3.0 19.1 1.0 OD2 B:ASP170 3.1 20.7 1.0 CG B:HIS172 3.1 18.4 1.0 OD1 B:ASP259 3.4 19.9 1.0 CB B:HIS172 3.5 17.9 1.0 N B:HIS172 3.8 18.6 1.0 CA B:GLY296 4.1 22.9 1.0 CG2 B:ILE171 4.1 17.9 1.0 NE2 B:HIS172 4.1 18.2 1.0 CH3 B:ACT501 4.2 23.4 1.0 CB B:ASP170 4.2 19.1 1.0 CD2 B:HIS172 4.2 18.7 1.0 CB B:ASP259 4.3 18.8 1.0 N B:ILE171 4.3 18.3 1.0 CA B:HIS172 4.3 18.3 1.0 NE2 B:HIS134 4.4 19.4 1.0 CE2 B:TYR298 4.4 18.2 1.0 OH B:TYR298 4.5 19.1 1.0 N B:GLY296 4.5 23.4 1.0 NE2 B:HIS135 4.6 15.4 1.0 C B:ILE171 4.8 18.2 1.0 C B:ASP170 4.9 19.0 1.0 CE1 B:HIS134 4.9 19.2 1.0 CA B:ASP170 4.9 19.1 1.0 CA B:ILE171 4.9 18.3 1.0 CZ B:TYR298 5.0 18.8 1.0

P.J.Watson, L.Fairall, G.M.Santos, J.W.R.Schwabe. Structure of HDAC3 Bound to Co-Repressor and Inositol Tetraphosphate. Nature V. 481 335 2012.
ISSN: ISSN 0028-0836
PubMed: 22230954
DOI: 10.1038/NATURE10728