Zinc in PDB 5wgm: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083, PDB code: 5wgm 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)	49.95 / 1.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	97.813, 174.304, 149.064, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.5

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Potassium	(K)	6 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 (pdb code 5wgm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083, PDB code: 5wgm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:13.0 occ:1.00 O04 A:AH7804 1.9 35.8 1.0 OD2 A:ASP705 2.0 9.3 1.0 OD1 A:ASP612 2.0 9.0 1.0 O A:HOH923 2.0 14.6 1.0 ND1 A:HIS614 2.1 7.8 1.0 N03 A:AH7804 2.5 13.1 1.0 CG A:ASP612 2.7 9.3 1.0 OD2 A:ASP612 2.8 9.3 1.0 CG A:ASP705 3.0 9.2 1.0 CE1 A:HIS614 3.0 10.7 1.0 CG A:HIS614 3.2 8.0 1.0 OD1 A:ASP705 3.3 8.3 1.0 C02 A:AH7804 3.5 17.2 1.0 CB A:HIS614 3.5 6.9 1.0 O01 A:AH7804 3.9 24.4 1.0 N A:HIS614 3.9 8.2 1.0 NE2 A:HIS573 4.1 8.8 1.0 NE2 A:HIS614 4.2 8.4 1.0 CB A:ASP612 4.2 8.8 1.0 CG1 A:VAL613 4.2 7.6 1.0 CD2 A:HIS614 4.3 8.0 1.0 CB A:ASP705 4.3 8.0 1.0 CA A:HIS614 4.4 10.9 1.0 N A:VAL613 4.4 7.2 1.0 CA A:GLY743 4.4 10.1 1.0 OH A:TYR745 4.5 15.6 1.0 CE1 A:HIS573 4.5 8.8 1.0 NE2 A:HIS574 4.5 12.4 1.0 C05 A:AH7804 4.6 15.5 1.0 CE2 A:TYR745 4.6 12.4 1.0 N A:GLY743 4.8 9.7 1.0 C A:VAL613 4.9 8.4 1.0 C A:ASP612 4.9 7.3 1.0 CA A:ASP612 4.9 8.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:13.4 occ:1.00 O04 B:AH7804 1.9 32.2 1.0 OD1 B:ASP612 2.0 9.6 1.0 OD2 B:ASP705 2.0 9.4 1.0 O B:HOH901 2.1 17.3 1.0 ND1 B:HIS614 2.1 9.1 1.0 N03 B:AH7804 2.5 17.9 1.0 CG B:ASP612 2.7 11.6 1.0 OD2 B:ASP612 2.8 9.5 1.0 CE1 B:HIS614 2.9 11.7 1.0 CG B:ASP705 3.0 11.3 1.0 CG B:HIS614 3.2 11.3 1.0 OD1 B:ASP705 3.3 9.0 1.0 C02 B:AH7804 3.5 18.9 1.0 CB B:HIS614 3.6 10.8 1.0 O01 B:AH7804 3.9 26.1 1.0 N B:HIS614 3.9 8.1 1.0 NE2 B:HIS614 4.1 10.9 1.0 NE2 B:HIS573 4.1 12.7 1.0 CB B:ASP612 4.2 7.8 1.0 CG1 B:VAL613 4.3 10.5 1.0 CD2 B:HIS614 4.3 10.5 1.0 CA B:GLY743 4.3 8.6 1.0 CB B:ASP705 4.3 7.8 1.0 N B:VAL613 4.4 7.5 1.0 OH B:TYR745 4.4 16.1 1.0 CA B:HIS614 4.4 10.1 1.0 CE1 B:HIS573 4.6 9.7 1.0 NE2 B:HIS574 4.6 12.2 1.0 CE2 B:TYR745 4.6 9.4 1.0 C05 B:AH7804 4.6 17.4 1.0 N B:GLY743 4.7 8.6 1.0 C B:ASP612 4.9 9.3 1.0 C B:VAL613 4.9 9.1 1.0 CA B:ASP612 4.9 8.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:13.6 occ:1.00 O04 C:AH7804 1.9 35.5 1.0 OD1 C:ASP612 2.0 10.1 1.0 OD2 C:ASP705 2.0 10.4 1.0 O C:HOH907 2.1 15.3 1.0 ND1 C:HIS614 2.1 9.8 1.0 N03 C:AH7804 2.5 13.7 1.0 CG C:ASP612 2.7 12.2 1.0 OD2 C:ASP612 2.7 11.2 1.0 CE1 C:HIS614 3.0 10.7 1.0 CG C:ASP705 3.0 11.7 1.0 CG C:HIS614 3.2 12.8 1.0 OD1 C:ASP705 3.4 10.9 1.0 C02 C:AH7804 3.4 20.4 1.0 CB C:HIS614 3.6 11.4 1.0 O01 C:AH7804 3.8 24.4 1.0 N C:HIS614 3.9 8.1 1.0 NE2 C:HIS573 4.1 13.2 1.0 CB C:ASP612 4.1 11.9 1.0 NE2 C:HIS614 4.2 10.3 1.0 CG1 C:VAL613 4.2 9.1 1.0 CD2 C:HIS614 4.3 12.0 1.0 CA C:GLY743 4.4 9.1 1.0 CA C:HIS614 4.4 10.2 1.0 CB C:ASP705 4.4 11.1 1.0 N C:VAL613 4.4 9.3 1.0 OH C:TYR745 4.5 15.5 1.0 CE1 C:HIS573 4.5 11.4 1.0 C05 C:AH7804 4.5 14.7 1.0 NE2 C:HIS574 4.6 12.5 1.0 CE2 C:TYR745 4.6 13.2 1.0 N C:GLY743 4.8 9.0 1.0 C C:VAL613 4.9 9.8 1.0 C C:ASP612 4.9 7.5 1.0 CA C:ASP612 4.9 7.6 1.0 C25 C:AH7804 5.0 20.1 1.0

N.J.Porter, A.Mahendran, R.Breslow, D.W.Christianson. Unusual Zinc-Binding Mode of HDAC6-Selective Hydroxamate Inhibitors. Proc. Natl. Acad. Sci. V. 114 13459 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29203661
DOI: 10.1073/PNAS.1718823114