Zinc in PDB 6whn: Histone Deacetylases Complex with Peptide Macrocycles

All present enzymatic activity of Histone Deacetylases Complex with Peptide Macrocycles:
3.5.1.98;

The structure of Histone Deacetylases Complex with Peptide Macrocycles, PDB code: 6whn was solved by A.K.Bera, P.Hosseinzadeh, P.Watson, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.82 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.349, 97.665, 138.989, 90, 90, 90
R / Rfree (%)	16.3 / 19.2

The structure of Histone Deacetylases Complex with Peptide Macrocycles also contains other interesting chemical elements:

Sodium

(Na)

6 atoms

The binding sites of Zinc atom in the Histone Deacetylases Complex with Peptide Macrocycles (pdb code 6whn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Histone Deacetylases Complex with Peptide Macrocycles, PDB code: 6whn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.1 occ:1.00 OD2 A:ASP269 1.9 12.5 1.0 OD2 A:ASP181 2.0 12.2 1.0 ND1 A:HIS183 2.0 12.7 1.0 SH F:U2M500 2.3 13.8 1.0 CG A:ASP181 2.8 13.3 1.0 CE1 A:HIS183 2.8 12.4 1.0 CG A:ASP269 2.9 12.0 1.0 OD1 A:ASP181 3.0 12.7 1.0 CG A:HIS183 3.2 13.6 1.0 CZ F:U2M500 3.2 18.7 1.0 OD1 A:ASP269 3.2 11.2 1.0 CB A:HIS183 3.6 13.4 1.0 CE F:U2M500 3.7 15.4 1.0 N A:HIS183 3.9 10.9 1.0 NE2 A:HIS183 4.0 15.3 1.0 NE2 A:HIS145 4.1 14.1 1.0 CA A:GLY306 4.1 14.3 1.0 CG2 A:ILE182 4.2 11.8 1.0 CD2 A:HIS183 4.2 14.3 1.0 CB A:ASP181 4.2 11.4 1.0 CB A:ASP269 4.3 11.5 1.0 CA A:HIS183 4.4 12.2 1.0 CE1 A:TYR308 4.4 12.1 1.0 N A:ILE182 4.4 10.8 1.0 N A:GLY306 4.5 13.2 1.0 CE1 A:HIS145 4.5 13.0 1.0 NE2 A:HIS146 4.5 13.8 1.0 OH A:TYR308 4.6 13.7 1.0 C A:ILE182 4.9 12.0 1.0 CA A:ASP181 4.9 10.2 1.0 C A:ASP181 4.9 11.8 1.0 CZ A:TYR308 5.0 13.6 1.0

Zinc binding site 2 out of 3 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:11.0 occ:1.00 OD2 B:ASP181 1.9 10.8 1.0 OD2 B:ASP269 2.0 10.4 1.0 ND1 B:HIS183 2.0 9.4 1.0 SH G:U2M500 2.3 12.2 1.0 CG B:ASP181 2.8 12.6 1.0 CE1 B:HIS183 2.9 14.5 1.0 CG B:ASP269 2.9 9.8 1.0 OD1 B:ASP181 3.0 11.0 1.0 CG B:HIS183 3.1 11.5 1.0 OD1 B:ASP269 3.3 10.5 1.0 CZ G:U2M500 3.3 17.6 1.0 CB B:HIS183 3.6 11.0 1.0 N B:HIS183 3.9 8.4 1.0 CE G:U2M500 3.9 17.0 1.0 NE2 B:HIS183 4.1 12.3 1.0 NE2 B:HIS145 4.1 10.7 1.0 CA B:GLY306 4.2 10.7 1.0 CD2 B:HIS183 4.2 12.1 1.0 CB B:ASP181 4.2 9.8 1.0 CG2 B:ILE182 4.2 11.4 1.0 CB B:ASP269 4.3 8.3 1.0 CE1 B:TYR308 4.3 10.9 1.0 CA B:HIS183 4.4 10.0 1.0 N B:ILE182 4.4 9.0 1.0 NE2 B:HIS146 4.5 10.3 1.0 CE1 B:HIS145 4.5 9.9 1.0 N B:GLY306 4.6 10.4 1.0 OH B:TYR308 4.6 11.3 1.0 C B:ILE182 4.9 11.7 1.0 CA B:ASP181 4.9 8.2 1.0 C B:ASP181 4.9 10.0 1.0 CZ B:TYR308 5.0 9.6 1.0

Zinc binding site 3 out of 3 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:15.3 occ:0.89 OD2 C:ASP269 2.0 15.3 1.0 OD2 C:ASP181 2.0 15.1 1.0 ND1 C:HIS183 2.1 19.0 1.0 SH H:U2M500 2.2 16.5 1.0 CG C:ASP181 2.8 13.1 1.0 CE1 C:HIS183 3.0 15.1 1.0 CG C:ASP269 3.0 16.9 1.0 OD1 C:ASP181 3.0 16.2 1.0 CZ H:U2M500 3.1 19.0 1.0 CG C:HIS183 3.1 16.0 1.0 OD1 C:ASP269 3.3 18.0 1.0 CB C:HIS183 3.6 15.4 1.0 CE H:U2M500 3.8 18.5 1.0 N C:HIS183 3.9 15.8 1.0 NE2 C:HIS183 4.1 17.9 1.0 NE2 C:HIS145 4.1 19.5 1.0 CA C:GLY306 4.1 18.4 1.0 CG2 C:ILE182 4.2 18.5 1.0 CD2 C:HIS183 4.2 19.2 1.0 CB C:ASP181 4.2 16.1 1.0 CB C:ASP269 4.3 21.3 1.0 CE1 C:TYR308 4.4 17.7 1.0 CA C:HIS183 4.4 16.0 1.0 N C:ILE182 4.4 16.3 1.0 CE1 C:HIS145 4.5 17.7 1.0 NE2 C:HIS146 4.5 16.8 1.0 OH C:TYR308 4.6 19.6 1.0 N C:GLY306 4.6 17.3 1.0 C C:ILE182 4.9 15.0 1.0 C C:ASP181 5.0 16.6 1.0 CA C:ASP181 5.0 16.5 1.0 CZ C:TYR308 5.0 22.3 1.0

A.K.Bera, P.Hosseinzadeh, D.Baker. Anchor Extension, A Structure-Guided Approach to Design Macrocycles Targeting Histone Deacetylases To Be Published.