Zinc in PDB 5dc5: Crystal Structure of D176N HDAC8 in Complex with M344

All present enzymatic activity of Crystal Structure of D176N HDAC8 in Complex with M344:
3.5.1.98;

The structure of Crystal Structure of D176N HDAC8 in Complex with M344, PDB code: 5dc5 was solved by C.Decroos, M.S.Lee, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.50 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.487, 83.025, 94.402, 90.00, 97.14, 90.00
R / Rfree (%)	18.2 / 21

The structure of Crystal Structure of D176N HDAC8 in Complex with M344 also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of D176N HDAC8 in Complex with M344 (pdb code 5dc5). 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 D176N HDAC8 in Complex with M344, PDB code: 5dc5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of D176N HDAC8 in Complex with M344


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 D176N HDAC8 in Complex with M344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:26.4 occ:1.00 OD2 A:ASP267 1.9 24.7 1.0 OD2 A:ASP178 2.0 29.3 1.0 ND1 A:HIS180 2.1 21.7 1.0 O4 A:B3N402 2.2 29.4 1.0 O2 A:B3N402 2.3 25.4 1.0 N3 A:B3N402 2.9 25.7 1.0 CG A:ASP178 2.9 28.6 1.0 C1 A:B3N402 2.9 30.7 1.0 CG A:ASP267 3.0 25.3 1.0 CE1 A:HIS180 3.0 21.2 1.0 OD1 A:ASP178 3.1 28.4 1.0 CG A:HIS180 3.1 23.9 1.0 OD1 A:ASP267 3.4 23.1 1.0 CB A:HIS180 3.5 22.8 1.0 N A:HIS180 3.7 21.0 1.0 CA A:GLY304 3.8 21.3 1.0 N A:GLY304 4.0 26.2 1.0 N A:LEU179 4.1 24.0 1.0 NE2 A:HIS180 4.1 22.0 1.0 CA A:HIS180 4.2 22.2 1.0 CD2 A:HIS180 4.2 20.5 1.0 CB A:ASP178 4.3 25.9 1.0 C5 A:B3N402 4.3 24.9 1.0 CB A:ASP267 4.3 22.6 1.0 CB A:LEU179 4.4 17.3 1.0 C6 A:B3N402 4.5 28.5 1.0 C A:LEU179 4.6 20.7 1.0 CA A:LEU179 4.6 19.1 1.0 NE2 A:HIS142 4.6 30.9 1.0 OH A:TYR306 4.8 27.9 1.0 CE1 A:TYR306 4.8 21.4 1.0 C A:ASP178 4.9 27.9 1.0 C A:GLY304 5.0 21.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of D176N HDAC8 in Complex with M344


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 D176N HDAC8 in Complex with M344 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:28.8 occ:1.00 OD2 B:ASP267 2.0 26.4 1.0 OD1 B:ASP178 2.1 30.9 1.0 ND1 B:HIS180 2.1 29.3 1.0 O4 B:B3N403 2.1 32.4 1.0 O2 B:B3N403 2.2 25.4 1.0 C1 B:B3N403 2.8 29.5 1.0 N3 B:B3N403 2.8 28.3 1.0 CG B:ASP178 2.9 31.4 1.0 CE1 B:HIS180 3.0 26.7 1.0 CG B:ASP267 3.1 26.4 1.0 CG B:HIS180 3.1 28.5 1.0 OD2 B:ASP178 3.2 32.8 1.0 OD1 B:ASP267 3.4 28.3 1.0 CB B:HIS180 3.5 25.4 1.0 N B:HIS180 3.7 27.1 1.0 CA B:GLY304 3.9 25.3 1.0 N B:GLY304 4.0 25.1 1.0 NE2 B:HIS180 4.1 27.6 1.0 N B:LEU179 4.2 26.1 1.0 C5 B:B3N403 4.2 27.2 1.0 CD2 B:HIS180 4.2 27.5 1.0 CA B:HIS180 4.2 27.9 1.0 CB B:ASP178 4.3 31.4 1.0 CB B:ASP267 4.4 26.2 1.0 CB B:LEU179 4.4 28.7 1.0 C6 B:B3N403 4.5 28.0 1.0 C B:LEU179 4.6 27.8 1.0 NE2 B:HIS142 4.6 29.7 1.0 CA B:LEU179 4.6 30.9 1.0 OH B:TYR306 4.8 29.0 1.0 C B:ASP178 4.9 30.7 1.0 CE1 B:TYR306 4.9 27.5 1.0 C B:GLY304 4.9 24.1 1.0 CE1 B:HIS142 5.0 31.0 1.0

S.M.Gantt, C.Decroos, M.S.Lee, L.E.Gullett, C.M.Bowman, D.W.Christianson, C.A.Fierke. General Base-General Acid Catalysis in Human Histone Deacetylase 8. Biochemistry V. 55 820 2016.
ISSN: ISSN 0006-2960
PubMed: 26806311
DOI: 10.1021/ACS.BIOCHEM.5B01327