Zinc in PDB 5iwg: HDAC2 with Ligand BRD4884

All present enzymatic activity of HDAC2 with Ligand BRD4884:
3.5.1.98;

The structure of HDAC2 with Ligand BRD4884, PDB code: 5iwg was solved by S.Steinbacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.297, 98.013, 139.250, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.8

The structure of HDAC2 with Ligand BRD4884 also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Calcium	(Ca)	6 atoms

The binding sites of Zinc atom in the HDAC2 with Ligand BRD4884 (pdb code 5iwg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the HDAC2 with Ligand BRD4884, PDB code: 5iwg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the HDAC2 with Ligand BRD4884


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HDAC2 with Ligand BRD4884 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.1 occ:1.00 OD2 A:ASP269 2.0 12.8 1.0 OD1 A:ASP181 2.0 12.0 1.0 N10 A:IWX403 2.1 11.8 1.0 ND1 A:HIS183 2.2 14.7 1.0 O1 A:IWX403 2.7 13.3 1.0 CG A:ASP181 2.8 11.8 1.0 CG A:ASP269 2.9 12.8 1.0 OD2 A:ASP181 3.0 11.6 1.0 CE1 A:HIS183 3.1 15.1 1.0 C9 A:IWX403 3.2 12.6 1.0 CG A:HIS183 3.2 14.9 1.0 OD1 A:ASP269 3.3 12.3 1.0 C2 A:IWX403 3.6 15.1 1.0 CB A:HIS183 3.6 14.2 1.0 C8 A:IWX403 3.9 11.6 1.0 N A:HIS183 4.0 13.5 1.0 C4 A:IWX403 4.0 13.2 1.0 N3 A:IWX403 4.1 14.6 1.0 CA A:GLY306 4.2 13.2 1.0 NE2 A:HIS183 4.2 15.6 1.0 CG2 A:ILE182 4.2 13.8 1.0 NE2 A:HIS145 4.2 14.7 1.0 CB A:ASP181 4.2 11.8 1.0 CD2 A:HIS183 4.3 15.4 1.0 CB A:ASP269 4.3 13.2 1.0 CA A:HIS183 4.4 13.9 1.0 N A:GLY306 4.4 12.9 1.0 C18 A:IWX403 4.6 16.7 1.0 N A:ILE182 4.6 12.5 1.0 NE2 A:HIS146 4.6 15.1 1.0 CE1 A:HIS145 4.7 14.1 1.0 OH A:TYR308 4.8 14.4 1.0 CE2 A:TYR308 4.9 14.2 1.0 C A:ILE182 5.0 13.4 1.0 CA A:ASP181 5.0 11.8 1.0

Zinc binding site 2 out of 3 in the HDAC2 with Ligand BRD4884


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of HDAC2 with Ligand BRD4884 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:10.4 occ:1.00 OD2 B:ASP269 1.9 9.9 1.0 OD1 B:ASP181 2.0 10.4 1.0 N10 B:IWX403 2.2 9.9 1.0 ND1 B:HIS183 2.2 12.0 1.0 O1 B:IWX403 2.8 11.9 1.0 CG B:ASP181 2.8 9.7 1.0 CG B:ASP269 2.9 10.1 1.0 OD2 B:ASP181 3.0 9.5 1.0 CE1 B:HIS183 3.0 12.6 1.0 C9 B:IWX403 3.2 10.2 1.0 CG B:HIS183 3.2 12.0 1.0 OD1 B:ASP269 3.2 9.6 1.0 CB B:HIS183 3.6 11.3 1.0 C2 B:IWX403 3.7 13.3 1.0 C8 B:IWX403 3.9 10.1 1.0 N B:HIS183 3.9 10.6 1.0 C4 B:IWX403 4.0 10.5 1.0 NE2 B:HIS183 4.2 13.5 1.0 N3 B:IWX403 4.2 12.1 1.0 CA B:GLY306 4.2 10.3 1.0 CB B:ASP181 4.2 9.6 1.0 NE2 B:HIS145 4.2 11.3 1.0 CB B:ASP269 4.3 10.3 1.0 CG2 B:ILE182 4.3 11.3 1.0 CD2 B:HIS183 4.3 13.2 1.0 CA B:HIS183 4.4 11.1 1.0 N B:GLY306 4.4 10.3 1.0 N B:ILE182 4.5 9.9 1.0 NE2 B:HIS146 4.6 12.8 1.0 CE1 B:HIS145 4.8 11.1 1.0 OH B:TYR308 4.9 11.9 1.0 C18 B:IWX403 4.9 16.6 1.0 CE2 B:TYR308 4.9 11.4 1.0 C B:ILE182 4.9 10.7 1.0 CA B:ASP181 5.0 9.5 1.0

Zinc binding site 3 out of 3 in the HDAC2 with Ligand BRD4884


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of HDAC2 with Ligand BRD4884 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:17.3 occ:1.00 OD2 C:ASP269 1.9 16.5 1.0 OD1 C:ASP181 2.0 17.7 1.0 N10 C:IWX403 2.2 14.7 1.0 ND1 C:HIS183 2.3 19.2 1.0 O1 C:IWX403 2.8 19.1 1.0 CG C:ASP181 2.8 17.7 1.0 CG C:ASP269 2.9 17.6 1.0 OD2 C:ASP181 2.9 17.9 1.0 CE1 C:HIS183 3.2 19.8 1.0 C9 C:IWX403 3.2 15.1 1.0 OD1 C:ASP269 3.2 17.4 1.0 CG C:HIS183 3.3 18.5 1.0 CB C:HIS183 3.6 17.6 1.0 C2 C:IWX403 3.7 19.9 1.0 N C:HIS183 3.9 17.8 1.0 C8 C:IWX403 4.0 14.8 1.0 C4 C:IWX403 4.0 15.7 1.0 N3 C:IWX403 4.2 17.6 1.0 CA C:GLY306 4.2 19.1 1.0 CG2 C:ILE182 4.2 19.4 1.0 NE2 C:HIS183 4.2 19.9 1.0 CB C:ASP269 4.3 18.4 1.0 CB C:ASP181 4.3 17.5 1.0 NE2 C:HIS145 4.3 18.2 1.0 CD2 C:HIS183 4.3 19.4 1.0 CA C:HIS183 4.4 17.5 1.0 N C:GLY306 4.4 18.5 1.0 N C:ILE182 4.5 18.3 1.0 NE2 C:HIS146 4.6 18.6 1.0 CE1 C:HIS145 4.8 18.1 1.0 C18 C:IWX403 4.9 21.1 1.0 C C:ILE182 4.9 18.2 1.0 OH C:TYR308 5.0 20.1 1.0 CA C:ASP181 5.0 17.9 1.0

F.F.Wagner, M.Weiwer, S.Steinbacher, A.Schomburg, P.Reinemer, J.P.Gale, A.J.Campbell, S.L.Fisher, W.N.Zhao, S.A.Reis, K.M.Hennig, M.Thomas, P.Muller, M.R.Jefson, D.M.Fass, S.J.Haggarty, Y.L.Zhang, E.B.Holson. Kinetic and Structural Insights Into the Binding of Histone Deacetylase 1 and 2 (HDAC1, 2) Inhibitors. Bioorg.Med.Chem. V. 24 4008 2016.
ISSN: ESSN 1464-3391
PubMed: 27377864
DOI: 10.1016/J.BMC.2016.06.040