Zinc in PDB 5tht: Crystal Structure of G303A HDAC8 in Complex with M344

All present enzymatic activity of Crystal Structure of G303A HDAC8 in Complex with M344:
3.5.1.98;

The structure of Crystal Structure of G303A HDAC8 in Complex with M344, PDB code: 5tht 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)	97.66 / 2.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	97.700, 83.810, 99.780, 90.00, 91.72, 90.00
R / Rfree (%)	18 / 21.2

The structure of Crystal Structure of G303A HDAC8 in Complex with M344 also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of G303A HDAC8 in Complex with M344 (pdb code 5tht). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of G303A HDAC8 in Complex with M344, PDB code: 5tht:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of G303A 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 G303A HDAC8 in Complex with M344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.5 occ:1.00 OD2 A:ASP267 2.0 14.4 1.0 O4 A:B3N401 2.0 25.1 1.0 OD2 A:ASP178 2.1 11.9 1.0 ND1 A:HIS180 2.2 14.1 1.0 O2 A:B3N401 2.2 17.4 1.0 N3 A:B3N401 2.8 19.8 1.0 C1 A:B3N401 2.8 21.4 1.0 CG A:ASP178 2.8 12.4 1.0 OD1 A:ASP178 2.9 14.5 1.0 CE1 A:HIS180 3.0 16.1 1.0 CG A:ASP267 3.1 16.4 1.0 CG A:HIS180 3.3 14.8 1.0 OD1 A:ASP267 3.6 16.5 1.0 CB A:HIS180 3.8 10.7 1.0 N A:HIS180 3.8 11.5 1.0 N A:LEU179 4.1 18.2 1.0 NE2 A:HIS180 4.1 15.3 1.0 C5 A:B3N401 4.2 23.9 1.0 CB A:ASP178 4.3 11.5 1.0 CD2 A:HIS180 4.3 12.4 1.0 CB A:LEU179 4.3 13.7 1.0 CB A:ASP267 4.4 12.6 1.0 OH A:TYR306 4.4 24.0 1.0 CA A:HIS180 4.4 14.5 1.0 C6 A:B3N401 4.6 24.0 1.0 CE1 A:TYR306 4.6 16.8 1.0 CA A:LEU179 4.6 14.3 1.0 CA A:GLY304 4.6 13.4 1.0 C A:LEU179 4.6 13.0 1.0 NE2 A:HIS142 4.7 12.4 1.0 O A:HOH560 4.7 27.4 1.0 C A:ASP178 4.9 12.7 1.0 CZ A:TYR306 5.0 21.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of G303A 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 G303A HDAC8 in Complex with M344 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:14.2 occ:1.00 OD2 B:ASP267 2.0 11.9 1.0 O4 B:B3N401 2.0 24.6 1.0 OD2 B:ASP178 2.0 10.9 1.0 O2 B:B3N401 2.1 25.4 1.0 ND1 B:HIS180 2.2 13.2 1.0 C1 B:B3N401 2.8 24.5 1.0 N3 B:B3N401 2.8 21.8 1.0 CG B:ASP178 2.8 12.5 1.0 OD1 B:ASP178 2.9 17.1 1.0 CE1 B:HIS180 2.9 15.0 1.0 CG B:ASP267 3.1 14.4 1.0 CG B:HIS180 3.3 14.9 1.0 OD1 B:ASP267 3.5 15.3 1.0 CB B:HIS180 3.8 11.9 1.0 N B:HIS180 3.8 9.5 1.0 NE2 B:HIS180 4.1 13.5 1.0 N B:LEU179 4.2 16.8 1.0 CB B:ASP178 4.3 12.7 1.0 C5 B:B3N401 4.3 30.4 1.0 CD2 B:HIS180 4.3 15.5 1.0 OH B:TYR306 4.3 23.7 1.0 CB B:ASP267 4.4 11.8 1.0 CB B:LEU179 4.4 10.2 1.0 CA B:HIS180 4.4 13.6 1.0 CE1 B:TYR306 4.5 20.5 1.0 CA B:LEU179 4.6 13.5 1.0 C B:LEU179 4.6 15.2 1.0 CA B:GLY304 4.7 13.8 1.0 C6 B:B3N401 4.7 28.5 1.0 NE2 B:HIS142 4.7 16.6 1.0 O B:HOH556 4.7 23.7 1.0 C B:ASP178 4.9 13.1 1.0 CZ B:TYR306 4.9 22.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of G303A 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 3 of Crystal Structure of G303A HDAC8 in Complex with M344 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:19.6 occ:1.00 OD2 C:ASP267 2.0 13.9 1.0 OD2 C:ASP178 2.0 16.5 1.0 O2 C:B3N401 2.1 28.0 1.0 ND1 C:HIS180 2.2 23.6 1.0 O4 C:B3N401 2.3 32.0 1.0 C1 C:B3N401 2.7 32.5 1.0 N3 C:B3N401 2.8 28.0 1.0 CG C:ASP178 2.9 17.6 1.0 CE1 C:HIS180 3.1 24.0 1.0 CG C:ASP267 3.1 18.8 1.0 OD1 C:ASP178 3.1 14.1 1.0 CG C:HIS180 3.2 20.9 1.0 OD1 C:ASP267 3.5 18.1 1.0 CB C:HIS180 3.6 21.4 1.0 N C:HIS180 3.7 16.0 1.0 C5 C:B3N401 4.0 51.1 1.0 C6 C:B3N401 4.1 41.3 1.0 N C:LEU179 4.1 14.4 1.0 NE2 C:HIS180 4.2 25.7 1.0 CA C:HIS180 4.3 16.0 1.0 CB C:ASP178 4.3 13.2 1.0 CD2 C:HIS180 4.3 21.0 1.0 CB C:ASP267 4.3 14.2 1.0 CB C:LEU179 4.4 17.0 1.0 OH C:TYR306 4.5 28.1 1.0 C C:LEU179 4.6 16.6 1.0 NE2 C:HIS142 4.6 11.9 1.0 CA C:LEU179 4.6 12.7 1.0 CE1 C:TYR306 4.6 20.9 1.0 CA C:GLY304 4.7 17.3 1.0 C C:ASP178 4.9 14.7 1.0 NE2 C:HIS143 4.9 22.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of G303A 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 4 of Crystal Structure of G303A HDAC8 in Complex with M344 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:21.3 occ:1.00 OD2 D:ASP267 1.9 16.7 1.0 OD2 D:ASP178 2.0 20.6 1.0 O2 D:B3N401 2.0 32.5 1.0 O4 D:B3N401 2.1 35.3 1.0 ND1 D:HIS180 2.1 25.1 1.0 C1 D:B3N401 2.6 41.2 1.0 N3 D:B3N401 2.7 33.7 1.0 CG D:ASP178 2.8 23.0 1.0 CE1 D:HIS180 3.0 24.4 1.0 OD1 D:ASP178 3.0 24.7 1.0 CG D:ASP267 3.0 19.4 1.0 CG D:HIS180 3.2 25.6 1.0 OD1 D:ASP267 3.5 22.0 1.0 CB D:HIS180 3.7 22.3 1.0 N D:HIS180 3.7 20.7 1.0 C5 D:B3N401 4.0 56.4 1.0 NE2 D:HIS180 4.1 23.8 1.0 N D:LEU179 4.2 19.5 1.0 CB D:ASP178 4.2 18.8 1.0 CD2 D:HIS180 4.3 25.3 1.0 CB D:ASP267 4.3 19.9 1.0 CA D:HIS180 4.3 25.4 1.0 C6 D:B3N401 4.4 44.5 1.0 CB D:LEU179 4.4 16.7 1.0 OH D:TYR306 4.6 24.0 1.0 NE2 D:HIS142 4.6 19.0 1.0 CE1 D:TYR306 4.6 22.9 1.0 C D:LEU179 4.6 26.7 1.0 CA D:LEU179 4.6 19.4 1.0 CA D:GLY304 4.6 18.8 1.0 C D:ASP178 4.9 23.2 1.0

N.J.Porter, N.H.Christianson, C.Decroos, D.W.Christianson. Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8. Biochemistry V. 55 6718 2016.
ISSN: ISSN 1520-4995
PubMed: 27933794
DOI: 10.1021/ACS.BIOCHEM.6B01014