Zinc in PDB 6csr: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate, PDB code: 6csr was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.20 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.890, 91.980, 96.400, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.9

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate (pdb code 6csr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate, PDB code: 6csr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:9.5 occ:1.00 OD2 A:ASP705 2.0 6.8 1.0 O2 A:BHO804 2.0 9.0 1.0 OD1 A:ASP612 2.0 4.2 1.0 ND1 A:HIS614 2.1 6.0 1.0 O1 A:BHO804 2.4 15.6 1.0 N A:BHO804 2.6 12.3 1.0 CG A:ASP612 2.7 5.0 1.0 OD2 A:ASP612 2.8 5.8 1.0 C A:BHO804 2.8 14.0 1.0 CE1 A:HIS614 2.9 6.7 1.0 CG A:ASP705 3.0 6.4 1.0 CG A:HIS614 3.2 6.5 1.0 OD1 A:ASP705 3.4 6.2 1.0 CB A:HIS614 3.6 5.7 1.0 N A:HIS614 3.9 4.4 1.0 NE2 A:HIS614 4.1 7.7 1.0 C1 A:BHO804 4.2 13.6 1.0 NE2 A:HIS573 4.2 6.2 1.0 CB A:ASP612 4.2 5.7 1.0 CD2 A:HIS614 4.2 7.2 1.0 CG1 A:VAL613 4.3 5.7 1.0 CA A:GLY743 4.3 4.9 1.0 CB A:ASP705 4.3 5.4 1.0 N A:VAL613 4.3 5.1 1.0 OH A:TYR745 4.4 10.4 1.0 CA A:HIS614 4.4 5.4 1.0 CE1 A:HIS573 4.5 6.4 1.0 CE2 A:TYR745 4.6 7.5 1.0 N A:GLY743 4.7 4.5 1.0 C6 A:BHO804 4.7 13.9 1.0 NE2 A:HIS574 4.7 5.4 1.0 O A:HOH1107 4.7 20.2 1.0 C A:VAL613 4.8 5.6 1.0 C A:ASP612 4.9 5.1 1.0 CA A:ASP612 4.9 5.0 1.0 CZ A:TYR745 5.0 9.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:8.9 occ:1.00 OD2 B:ASP705 2.0 7.2 1.0 O2 B:BHO804 2.0 10.6 1.0 OD1 B:ASP612 2.1 5.5 1.0 ND1 B:HIS614 2.1 6.0 1.0 O1 B:BHO804 2.4 12.1 1.0 N B:BHO804 2.6 12.5 1.0 CG B:ASP612 2.7 4.7 1.0 OD2 B:ASP612 2.8 5.1 1.0 C B:BHO804 2.8 12.6 1.0 CE1 B:HIS614 2.9 7.7 1.0 CG B:ASP705 3.0 6.5 1.0 CG B:HIS614 3.2 6.2 1.0 OD1 B:ASP705 3.4 6.4 1.0 CB B:HIS614 3.7 5.8 1.0 N B:HIS614 3.9 6.0 1.0 NE2 B:HIS614 4.1 7.8 1.0 C1 B:BHO804 4.1 12.0 1.0 NE2 B:HIS573 4.2 5.6 1.0 CB B:ASP612 4.2 3.3 1.0 CD2 B:HIS614 4.2 6.9 1.0 CG1 B:VAL613 4.3 4.0 1.0 CA B:GLY743 4.3 4.0 1.0 CB B:ASP705 4.3 5.5 1.0 N B:VAL613 4.3 4.6 1.0 CA B:HIS614 4.4 6.0 1.0 OH B:TYR745 4.4 9.5 1.0 CE1 B:HIS573 4.5 5.7 1.0 CE2 B:TYR745 4.6 8.6 1.0 O B:HOH1080 4.6 17.2 1.0 N B:GLY743 4.7 3.8 1.0 NE2 B:HIS574 4.7 5.0 1.0 C6 B:BHO804 4.7 11.9 1.0 C B:ASP612 4.9 5.2 1.0 C B:VAL613 4.9 6.4 1.0 CA B:ASP612 4.9 3.9 1.0 N B:GLY744 4.9 4.3 1.0 C B:GLY743 5.0 4.4 1.0

N.J.Porter, F.F.Wagner, D.W.Christianson. Entropy As A Driver of Selectivity For Inhibitor Binding to Histone Deacetylase 6. Biochemistry V. 57 3916 2018.
ISSN: ISSN 1520-4995
PubMed: 29775292
DOI: 10.1021/ACS.BIOCHEM.8B00367