Zinc in PDB 5wgi: Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa

The structure of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa, PDB code: 5wgi 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)	47.04 / 1.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.439, 69.639, 50.193, 90.00, 110.42, 90.00
R / Rfree (%)	10.6 / 12.6

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

Magnesium	(Mg)	1 atom
Potassium	(K)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Zinc atom in the Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa (pdb code 5wgi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa, PDB code: 5wgi:

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ultrahigh Resolution Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Tsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:6.9 occ:0.64 HO1 A:TSN802 1.7 22.1 0.3 HO1 A:TSN802 1.8 8.6 0.7 O1 A:TSN802 1.8 18.4 0.3 OD2 A:ASP705 2.0 6.8 1.0 O1 A:TSN802 2.0 7.2 0.7 OD1 A:ASP612 2.1 6.0 1.0 ND1 A:HIS614 2.1 6.1 1.0 O2 A:TSN802 2.2 8.3 0.7 N1 A:TSN802 2.3 15.3 0.3 HN1 A:TSN802 2.4 18.4 0.3 OD2 A:ASP612 2.6 7.2 1.0 N1 A:TSN802 2.7 10.4 0.7 CG A:ASP612 2.7 5.3 1.0 C13 A:TSN802 2.7 10.4 0.7 CG A:ASP705 3.0 6.1 1.0 CE1 A:HIS614 3.0 6.3 1.0 HB2 A:HIS614 3.1 6.7 1.0 HE1 A:HIS614 3.1 7.6 1.0 CG A:HIS614 3.2 5.4 1.0 H A:HIS614 3.3 6.4 1.0 HA3 A:GLY743 3.3 8.2 1.0 OD1 A:ASP705 3.4 6.5 1.0 HE2 A:HIS573 3.4 9.5 1.0 HN1 A:TSN802 3.4 12.5 0.7 C13 A:TSN802 3.5 13.3 0.3 HG12 A:VAL613 3.5 8.0 1.0 HH A:TYR745 3.6 11.4 1.0 CB A:HIS614 3.6 5.5 1.0 HE2 A:TYR745 3.8 9.9 1.0 O2 A:TSN802 4.0 12.0 0.3 N A:HIS614 4.0 5.3 1.0 H A:VAL613 4.0 6.1 1.0 H A:GLY743 4.1 7.5 1.0 C12 A:TSN802 4.1 9.3 0.7 CB A:ASP612 4.1 5.7 1.0 NE2 A:HIS573 4.1 7.9 1.0 NE2 A:HIS614 4.2 6.6 1.0 CA A:GLY743 4.3 6.9 1.0 H111 A:TSN802 4.3 11.2 0.7 HE1 A:HIS573 4.3 8.3 1.0 CD2 A:HIS614 4.3 6.0 1.0 CB A:ASP705 4.3 6.5 1.0 CG1 A:VAL613 4.4 6.6 1.0 HB3 A:HIS614 4.4 6.7 1.0 N A:VAL613 4.4 5.1 1.0 HG13 A:VAL613 4.4 8.0 1.0 OH A:TYR745 4.4 9.5 1.0 H111 A:TSN802 4.4 13.6 0.3 HB3 A:ASP612 4.5 6.8 1.0 CA A:HIS614 4.5 4.8 1.0 HB2 A:ASP705 4.5 7.8 1.0 HB3 A:ASP705 4.5 7.8 1.0 C12 A:TSN802 4.5 13.7 0.3 N A:GLY743 4.6 6.2 1.0 CE1 A:HIS573 4.6 6.9 1.0 HB2 A:ASP612 4.6 6.8 1.0 C11 A:TSN802 4.6 9.3 0.7 H A:GLY744 4.7 9.2 1.0 CE2 A:TYR745 4.7 8.2 1.0 NE2 A:HIS574 4.7 7.4 1.0 H121 A:TSN802 4.8 11.2 0.7 HA2 A:GLY743 4.8 8.2 1.0 C11 A:TSN802 4.8 11.3 0.3 HA A:ASP612 4.8 6.6 1.0 HA3 A:GLY703 4.8 7.3 1.0 C A:ASP612 4.9 5.0 1.0 CA A:ASP612 4.9 5.5 1.0 HG11 A:VAL613 4.9 8.0 1.0 HE2 A:HIS614 4.9 7.9 1.0 C A:VAL613 4.9 5.5 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