Zinc in PDB 5wgl: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215)

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215), PDB code: 5wgl 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)	49.30 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.189, 88.002, 119.025, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.9

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215) 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 Ricolinostat (Acy-1215) (pdb code 5wgl). 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 Ricolinostat (Acy-1215), PDB code: 5wgl:
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 Ricolinostat (Acy-1215)


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 Ricolinostat (Acy-1215) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:6.5 occ:1.00 O12 A:AH4804 2.0 9.1 0.5 O12 A:AH4804 2.0 9.1 0.5 OD2 A:ASP705 2.1 4.8 1.0 OD1 A:ASP612 2.1 6.1 1.0 ND1 A:HIS614 2.2 7.3 1.0 O13 A:AH4804 2.3 10.2 0.5 O13 A:AH4804 2.4 10.2 0.5 N11 A:AH4804 2.8 8.0 0.5 N11 A:AH4804 2.8 7.9 0.5 CG A:ASP612 2.8 5.5 1.0 OD2 A:ASP612 2.9 7.2 1.0 C10 A:AH4804 2.9 9.9 0.5 C10 A:AH4804 2.9 9.9 0.5 CG A:ASP705 3.1 6.7 1.0 CE1 A:HIS614 3.1 5.6 1.0 CG A:HIS614 3.3 5.8 1.0 OD1 A:ASP705 3.4 5.8 1.0 CB A:HIS614 3.7 6.4 1.0 N A:HIS614 4.0 6.1 1.0 NE2 A:HIS614 4.3 7.4 1.0 CA A:GLY743 4.3 3.4 1.0 CB A:ASP612 4.3 4.8 1.0 C09 A:AH4804 4.4 9.8 0.5 C09 A:AH4804 4.4 9.8 0.5 NE2 A:HIS573 4.4 6.8 1.0 CD2 A:HIS614 4.4 8.2 1.0 CG1 A:VAL613 4.4 5.3 1.0 CB A:ASP705 4.4 4.6 1.0 N A:VAL613 4.5 5.1 1.0 CA A:HIS614 4.5 4.6 1.0 OH A:TYR745 4.7 7.4 1.0 N A:GLY743 4.7 3.7 1.0 CE2 A:TYR745 4.8 5.8 1.0 C08 A:AH4804 4.9 8.9 0.5 CE1 A:HIS573 4.9 5.2 1.0 C08 A:AH4804 4.9 9.1 0.5 C A:VAL613 4.9 7.3 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 Ricolinostat (Acy-1215)


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 Ricolinostat (Acy-1215) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:7.4 occ:1.00 O12 B:AH4804 2.1 7.8 1.0 OD2 B:ASP705 2.1 6.4 1.0 OD1 B:ASP612 2.2 6.4 1.0 ND1 B:HIS614 2.2 6.8 1.0 O13 B:AH4804 2.3 9.0 1.0 OD2 B:ASP612 2.7 7.3 1.0 CG B:ASP612 2.8 8.7 1.0 N11 B:AH4804 2.8 8.4 1.0 C10 B:AH4804 2.9 12.7 1.0 CE1 B:HIS614 3.0 8.6 1.0 CG B:ASP705 3.1 8.6 1.0 CG B:HIS614 3.3 7.6 1.0 OD1 B:ASP705 3.4 6.0 1.0 CB B:HIS614 3.8 6.9 1.0 N B:HIS614 4.1 7.6 1.0 NE2 B:HIS614 4.2 8.7 1.0 CA B:GLY743 4.3 7.0 1.0 CB B:ASP612 4.3 6.2 1.0 C09 B:AH4804 4.3 11.0 1.0 CD2 B:HIS614 4.4 6.0 1.0 CG1 B:VAL613 4.4 7.0 1.0 NE2 B:HIS573 4.4 7.6 1.0 CB B:ASP705 4.5 6.8 1.0 N B:VAL613 4.5 5.3 1.0 CA B:HIS614 4.5 5.7 1.0 N B:GLY743 4.7 4.9 1.0 C08 B:AH4804 4.8 9.6 1.0 OH B:TYR745 4.8 9.7 1.0 CE2 B:TYR745 4.8 7.5 1.0 CE1 B:HIS573 4.8 7.4 1.0 C B:VAL613 5.0 4.9 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