Zinc in PDB 5zoo: Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment

All present enzymatic activity of Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment:
3.5.1.98;

The structure of Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment, PDB code: 5zoo was solved by S.Y.Park, H.J.Hwang, J.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.99 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.424, 131.424, 67.770, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 17.5

The structure of Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment (pdb code 5zoo). 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 Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment, PDB code: 5zoo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment


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 Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1103 b:26.2 occ:1.00 OD2 G:ASP934 2.0 23.3 1.0 OD1 G:ASP840 2.1 20.8 1.0 ND1 G:HIS842 2.1 19.8 1.0 O G:HOH1201 2.2 26.8 1.0 O G:HOH1224 2.2 24.2 1.0 OD2 G:ASP840 2.6 20.0 1.0 CG G:ASP840 2.6 21.3 1.0 CE1 G:HIS842 3.0 19.9 1.0 CG G:ASP934 3.0 27.5 1.0 CG G:HIS842 3.2 23.9 1.0 OD1 G:ASP934 3.4 23.0 1.0 CB G:HIS842 3.7 21.6 1.0 N G:HIS842 4.0 18.8 1.0 CB G:ASP840 4.1 17.3 1.0 O G:HOH1348 4.1 40.3 1.0 CA G:GLY974 4.1 20.6 1.0 NE2 G:HIS842 4.2 22.1 1.0 NE2 G:HIS802 4.3 22.2 1.0 CD2 G:HIS842 4.3 21.2 1.0 CG1 G:VAL841 4.3 20.3 1.0 OH G:TYR976 4.3 35.8 1.0 N G:VAL841 4.4 19.6 1.0 CB G:ASP934 4.4 24.6 1.0 CA G:HIS842 4.5 21.1 1.0 NE2 G:HIS803 4.5 23.0 1.0 N G:GLY974 4.5 21.9 1.0 CD1 A:ILE1363 4.6 23.2 1.0 CE2 G:TYR976 4.6 27.3 1.0 CE1 G:HIS802 4.7 20.8 1.0 C G:ASP840 4.8 20.9 1.0 CA G:ASP840 4.9 18.5 1.0 C G:GLY974 4.9 25.4 1.0 C G:VAL841 4.9 22.9 1.0 N G:GLY975 4.9 29.0 1.0 CZ G:TYR976 5.0 27.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment


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 Histone Deacetylase 4 (HDAC4) in Complex with A Smrt Corepressor SP1 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1104 b:28.7 occ:1.00 NE2 G:HIS675 2.0 27.1 1.0 SG G:CYS669 2.2 32.5 1.0 SG G:CYS751 2.3 26.3 1.0 SG G:CYS667 2.3 27.1 1.0 CE1 G:HIS675 2.9 27.3 1.0 CB G:CYS669 3.0 33.2 1.0 CD2 G:HIS675 3.1 23.8 1.0 CB G:CYS751 3.2 25.9 1.0 CB G:CYS667 3.2 26.3 1.0 ND1 G:HIS675 4.1 26.4 1.0 CG G:HIS675 4.2 25.4 1.0 N G:CYS669 4.2 29.5 1.0 CA G:CYS669 4.2 35.5 1.0 N G:GLY753 4.4 27.1 1.0 CA G:CYS751 4.6 32.4 1.0 CA G:GLY753 4.6 31.2 1.0 CA G:CYS667 4.6 25.8 1.0 CG2 G:ILE761 4.7 29.4 1.0 C G:CYS751 4.7 33.7 1.0 O G:CYS751 4.9 30.7 1.0 C G:CYS667 5.0 29.0 1.0

S.Y.Park, G.S.Kim, H.J.Hwang, T.H.Nam, H.S.Park, J.Song, T.H.Jang, Y.C.Lee, J.S.Kim. Structural Basis of the Specific Interaction of Smrt Corepressor with Histone Deacetylase 4. Nucleic Acids Res. V. 46 11776 2018.
ISSN: ESSN 1362-4962
PubMed: 30321390
DOI: 10.1093/NAR/GKY926