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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5zoo:

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

Zinc Binding Sites:

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 5zoo

Go back to Zinc Binding Sites List in 5zoo
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 5zoo

Go back to Zinc Binding Sites List in 5zoo
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

Reference:

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
Page generated: Wed Dec 16 11:27:37 2020

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