Zinc in PDB 6z6h: Hdac-Dc

All present enzymatic activity of Hdac-Dc:
3.5.1.98;

The binding sites of Zinc atom in the Hdac-Dc (pdb code 6z6h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Hdac-Dc, PDB code: 6z6h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Hdac-Dc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hdac-Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:1000.0 occ:1.00 OD2 A:ASP245 2.2 1000.0 1.0 CA A:GLY376 2.7 978.8 1.0 N A:GLY376 2.9 978.8 1.0 CG A:ASP245 3.1 1000.0 1.0 C A:GLU375 3.3 1000.0 1.0 OD1 A:ASP245 3.3 1000.0 1.0 NE2 A:HIS205 3.4 804.4 1.0 O A:GLU375 3.5 1000.0 1.0 OD2 A:ASP338 3.7 1000.0 1.0 CB A:GLU375 3.8 1000.0 1.0 CG A:ASP338 4.0 1000.0 1.0 CD2 A:HIS205 4.0 804.4 1.0 OD1 A:ASP338 4.1 1000.0 1.0 C A:GLY376 4.1 978.8 1.0 CA A:GLU375 4.2 1000.0 1.0 CB A:ASP245 4.5 1000.0 1.0 CE1 A:HIS205 4.5 804.4 1.0 N A:GLY377 4.5 902.0 1.0 ND1 A:HIS247 4.7 809.5 1.0 CB A:ASP338 4.7 1000.0 1.0 CA A:GLY336 5.0 1000.0 1.0

Zinc binding site 2 out of 4 in the Hdac-Dc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hdac-Dc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:799.6 occ:1.00 OD1 B:ASP245 2.3 856.4 1.0 ND1 B:HIS247 2.3 794.5 1.0 NE2 B:HIS205 2.3 960.0 1.0 CE1 B:HIS205 2.4 960.0 1.0 CB B:HIS247 2.8 794.5 1.0 CG B:HIS247 2.8 794.5 1.0 CG B:ASP245 3.0 856.4 1.0 OD2 B:ASP245 3.1 856.4 1.0 CE1 B:HIS247 3.5 794.5 1.0 OD2 B:ASP338 3.6 719.4 1.0 CD2 B:HIS205 3.7 960.0 1.0 NE2 B:HIS206 3.7 956.4 1.0 ND1 B:HIS205 3.7 960.0 1.0 OH B:TYR378 3.8 581.1 1.0 CA B:HIS247 3.8 794.5 1.0 N B:HIS247 3.9 794.5 1.0 CD2 B:HIS247 4.1 794.5 1.0 O B:HIS247 4.2 794.5 1.0 CE1 B:HIS206 4.3 956.4 1.0 C B:HIS247 4.3 794.5 1.0 CG B:HIS205 4.3 960.0 1.0 NE2 B:HIS247 4.3 794.5 1.0 CD2 B:HIS206 4.4 956.4 1.0 CB B:ASP245 4.4 856.4 1.0 CG B:ASP338 4.8 719.4 1.0 CZ B:TYR378 4.8 581.1 1.0 CE2 B:TYR378 4.9 581.1 1.0 CA B:GLY376 5.0 754.3 1.0

Zinc binding site 3 out of 4 in the Hdac-Dc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hdac-Dc within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn801 b:1000.0 occ:1.00 NE2 F:HIS205 2.3 941.7 1.0 NE2 F:HIS206 2.4 793.5 1.0 CD2 F:HIS206 2.4 793.5 1.0 CE1 F:HIS205 2.7 941.7 1.0 ND1 F:HIS247 3.4 852.8 1.0 CD2 F:HIS205 3.4 941.7 1.0 CE1 F:HIS206 3.6 793.5 1.0 CG F:HIS206 3.7 793.5 1.0 OD1 F:ASP245 3.8 1000.0 1.0 ND1 F:HIS205 3.9 941.7 1.0 CB F:HIS247 4.0 852.8 1.0 CG F:HIS247 4.1 852.8 1.0 ND1 F:HIS206 4.2 793.5 1.0 CG F:HIS205 4.3 941.7 1.0 CE1 F:HIS247 4.3 852.8 1.0 O F:GLY214 4.3 801.0 1.0 CG F:ASP245 4.4 1000.0 1.0 OD2 F:ASP245 4.5 1000.0 1.0 CB F:HIS206 4.8 793.5 1.0

Zinc binding site 4 out of 4 in the Hdac-Dc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hdac-Dc within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn801 b:805.9 occ:1.00 OD1 G:ASP245 2.2 892.9 1.0 ND1 G:HIS247 2.3 835.4 1.0 CE1 G:HIS205 2.4 1000.0 1.0 CB G:HIS247 2.6 835.4 1.0 NE2 G:HIS205 2.7 1000.0 1.0 CG G:HIS247 2.8 835.4 1.0 CG G:ASP245 3.0 892.9 1.0 OD2 G:ASP338 3.2 779.5 1.0 OD2 G:ASP245 3.2 892.9 1.0 CE1 G:HIS247 3.5 835.4 1.0 N G:HIS247 3.6 835.4 1.0 CA G:HIS247 3.6 835.4 1.0 ND1 G:HIS205 3.6 1000.0 1.0 CD2 G:HIS205 4.0 1000.0 1.0 O G:HIS247 4.1 835.4 1.0 CD2 G:HIS247 4.1 835.4 1.0 NE2 G:HIS206 4.1 1000.0 1.0 C G:HIS247 4.2 835.4 1.0 CG G:ASP338 4.3 779.5 1.0 CB G:ASP245 4.3 892.9 1.0 NE2 G:HIS247 4.4 835.4 1.0 CG G:HIS205 4.5 1000.0 1.0 OH G:TYR378 4.5 645.2 1.0 CE1 G:HIS206 4.5 1000.0 1.0 OD1 G:ASP338 4.6 779.5 1.0 C G:ILE246 4.8 851.5 1.0 C G:ASP245 4.8 892.9 1.0 CA G:GLY376 4.9 833.0 1.0 N G:ILE246 4.9 851.5 1.0 CD2 G:HIS206 4.9 1000.0 1.0 CE2 G:TYR378 4.9 645.2 1.0

J.H.Lee, D.Bollschweiler, T.Schafer, R.Huber. Structural Basis For the Regulation of Nucleosome Recognition and Hdac Activity By Histone Deacetylase Assemblies. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33523989
DOI: 10.1126/SCIADV.ABD4413