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Zinc in PDB 6wdw: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor, PDB code: 6wdw was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.14 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.563, 80.563, 246.907, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 23.6

Other elements in 6wdw:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor (pdb code 6wdw). 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 Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor, PDB code: 6wdw:

Zinc binding site 1 out of 1 in 6wdw

Go back to Zinc Binding Sites List in 6wdw
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor


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 Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:33.7
occ:1.00
 OD2 A:ASP174 2.0 25.1 1.0
OD2 A:ASP267 2.1 28.7 1.0
O25 A:TWV701 2.2 41.4 1.0
O01 A:TWV701 2.2 40.5 1.0
ND1 A:HIS176 2.2 31.1 1.0
C03 A:TWV701 2.6 41.8 1.0
N02 A:TWV701 2.7 40.0 1.0
CG A:ASP174 2.7 29.2 1.0
OD1 A:ASP174 2.7 29.9 1.0
CG A:ASP267 3.0 30.9 1.0
CE1 A:HIS176 3.2 31.3 1.0
CG A:HIS176 3.2 31.7 1.0
OD1 A:ASP267 3.3 27.4 1.0
CB A:HIS176 3.5 25.9 1.0
N A:HIS176 3.8 31.6 1.0
C04 A:TWV701 4.0 37.1 1.0
CB A:ASP174 4.2 24.4 1.0
N A:VAL175 4.2 30.8 1.0
CA A:HIS176 4.3 28.9 1.0
NE2 A:HIS176 4.3 30.4 1.0
NE2 A:HIS136 4.3 31.8 1.0
CD2 A:HIS176 4.3 32.5 1.0
CG1 A:VAL175 4.3 29.2 1.0
CB A:ASP267 4.4 31.0 1.0
CA A:GLY305 4.5 27.6 1.0
C05 A:TWV701 4.6 43.4 1.0
CE1 A:HIS136 4.6 26.3 1.0
OH A:TYR307 4.6 40.3 1.0
CE2 A:TYR307 4.7 34.6 1.0
C A:VAL175 4.7 31.9 1.0
N A:GLY305 4.8 33.1 1.0
NE2 A:HIS137 4.8 38.5 1.0
CA A:VAL175 4.9 31.1 1.0
C A:ASP174 4.9 30.3 1.0
CA A:ASP174 4.9 24.1 1.0

Reference:

C.J.Herbst-Gervasoni, R.R.Steimbach, M.Morgen, A.K.Miller, D.W.Christianson. Structural Basis For the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase. Acs Chem.Biol. V. 15 2154 2020.
ISSN: ESSN 1554-8937
PubMed: 32659072
DOI: 10.1021/ACSCHEMBIO.0C00362
Page generated: Tue Oct 29 09:18:52 2024

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