Zinc in PDB 5ikk: Structure of the Histone Deacetylase CLR3

All present enzymatic activity of Structure of the Histone Deacetylase CLR3:
3.5.1.98;

The structure of Structure of the Histone Deacetylase CLR3, PDB code: 5ikk was solved by C.Brugger, T.Schalch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.82 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.487, 187.259, 142.633, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.8

The structure of Structure of the Histone Deacetylase CLR3 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	2 atoms

The binding sites of Zinc atom in the Structure of the Histone Deacetylase CLR3 (pdb code 5ikk). 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 the Histone Deacetylase CLR3, PDB code: 5ikk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Histone Deacetylase CLR3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Histone Deacetylase CLR3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:21.9 occ:1.00 HE1 A:HIS195 1.9 44.7 1.0 OD2 A:ASP327 2.0 21.2 1.0 NE2 A:HIS195 2.0 39.4 1.0 ND1 A:HIS236 2.0 23.5 1.0 OD1 A:ASP234 2.1 23.4 1.0 OD2 A:ASP234 2.1 20.1 1.0 CE1 A:HIS195 2.2 37.2 1.0 CG A:ASP234 2.4 19.4 1.0 CE1 A:HIS236 2.9 24.5 1.0 HE1 A:HIS236 3.0 29.4 1.0 CG A:ASP327 3.0 20.0 1.0 HB2 A:HIS236 3.1 28.2 1.0 H A:HIS236 3.1 25.0 1.0 CG A:HIS236 3.1 24.2 1.0 CD2 A:HIS195 3.3 38.4 1.0 OD1 A:ASP327 3.4 18.7 1.0 ND1 A:HIS195 3.5 35.5 1.0 HG22 A:ILE235 3.5 25.0 1.0 HA3 A:GLY365 3.6 26.3 1.0 CB A:HIS236 3.6 23.6 1.0 H A:ILE235 3.8 21.8 1.0 N A:HIS236 3.8 20.9 1.0 HD2 A:HIS195 3.9 46.1 1.0 CB A:ASP234 3.9 18.0 1.0 HB3 A:ALA196 4.0 76.4 1.0 CG A:HIS195 4.0 36.7 1.0 NE2 A:HIS236 4.1 25.8 1.0 CD2 A:HIS236 4.2 25.6 1.0 N A:ILE235 4.2 18.2 1.0 HB3 A:ASP234 4.3 21.6 1.0 HB2 A:ASP234 4.3 21.6 1.0 CA A:HIS236 4.3 22.4 1.0 CG2 A:ILE235 4.3 20.8 1.0 CB A:ASP327 4.3 20.4 1.0 HG23 A:ILE235 4.4 25.0 1.0 HB3 A:HIS236 4.4 28.2 1.0 HH A:TYR367 4.5 33.5 1.0 HE2 A:TYR367 4.5 30.8 1.0 HB3 A:ASP327 4.5 24.5 1.0 CA A:GLY365 4.5 21.9 1.0 H A:GLY365 4.5 25.3 1.0 HB2 A:ASP327 4.6 24.5 1.0 HB1 A:ALA196 4.7 76.4 1.0 HA A:ASP234 4.7 20.3 1.0 C A:ASP234 4.7 17.5 1.0 CA A:ASP234 4.7 16.9 1.0 CB A:ALA196 4.8 63.7 1.0 C A:ILE235 4.8 20.3 1.0 HG21 A:ILE235 4.9 25.0 1.0 O A:HOH995 4.9 41.4 1.0 H A:ASP327 5.0 21.6 1.0 CA A:ILE235 5.0 18.9 1.0 HA3 A:GLY325 5.0 20.1 1.0 N A:GLY365 5.0 21.1 1.0

Zinc binding site 2 out of 2 in the Structure of the Histone Deacetylase CLR3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Histone Deacetylase CLR3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:47.1 occ:1.00 HE1 A:HIS77 1.7 67.4 1.0 CE1 A:HIS77 2.0 56.2 1.0 NE2 A:HIS68 2.0 42.9 1.0 NE2 A:HIS77 2.0 55.0 1.0 SG A:CYS162 2.3 51.8 1.0 CE1 A:HIS68 3.0 41.8 1.0 CD2 A:HIS68 3.0 45.5 1.0 HB3 A:CYS162 3.1 51.7 1.0 ND1 A:HIS77 3.2 58.4 1.0 HE1 A:HIS68 3.2 50.2 1.0 HD2 A:HIS68 3.2 54.6 1.0 CD2 A:HIS77 3.3 55.1 1.0 CB A:CYS162 3.3 43.1 1.0 HB2 A:CYS162 3.6 51.7 1.0 O A:HOH1004 3.8 21.8 1.0 CG A:HIS77 3.8 58.4 1.0 HD2 A:HIS77 3.9 66.2 1.0 HA A:PRO192 4.1 46.7 1.0 ND1 A:HIS68 4.1 43.5 1.0 CG A:HIS68 4.1 45.5 1.0 HB3 A:PRO192 4.2 50.2 1.0 O A:ARG190 4.2 37.6 1.0 HE2 A:PHE67 4.4 62.5 1.0 O A:HOH883 4.5 20.4 1.0 CA A:CYS162 4.6 43.5 1.0 HA A:CYS162 4.7 52.2 1.0 CA A:PRO192 4.8 38.9 1.0 HB3 A:PRO81 4.8 48.4 1.0 O A:PRO191 4.9 35.5 1.0 O A:HOH896 4.9 44.6 1.0 N A:PRO192 4.9 37.2 1.0 CB A:PRO192 5.0 41.8 1.0 C A:PRO191 5.0 36.5 1.0

G.Job, C.Brugger, T.Xu, B.R.Lowe, Y.Pfister, C.Qu, S.Shanker, J.I.Banos Sanz, J.F.Partridge, T.Schalch. Shrec Silences Heterochromatin Via Distinct Remodeling and Deacetylation Modules. Mol.Cell V. 62 207 2016.
ISSN: ISSN 1097-2765
PubMed: 27105116
DOI: 10.1016/J.MOLCEL.2016.03.016