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

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

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminomethylindole 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 Dimethylaminomethylindole Phenylhydroxamate Inhibitor, PDB code: 6wdv 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) 69.86 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.670, 80.670, 246.842, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 22.7

Other elements in 6wdv:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminomethylindole 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 Dimethylaminomethylindole Phenylhydroxamate Inhibitor (pdb code 6wdv). 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 Dimethylaminomethylindole Phenylhydroxamate Inhibitor, PDB code: 6wdv:

Zinc binding site 1 out of 1 in 6wdv

Go back to Zinc Binding Sites List in 6wdv
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminomethylindole 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 Dimethylaminomethylindole Phenylhydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:42.2
occ:1.00
 O01 A:TWM701 2.0 42.5 1.0
OD2 A:ASP174 2.0 35.7 1.0
OD2 A:ASP267 2.0 38.5 1.0
ND1 A:HIS176 2.2 39.6 1.0
N02 A:TWM701 2.3 46.9 1.0
O24 A:TWM701 2.5 51.1 1.0
C03 A:TWM701 2.7 46.4 1.0
CG A:ASP174 2.7 39.8 1.0
OD1 A:ASP174 2.8 37.3 1.0
CG A:ASP267 3.0 43.5 1.0
CE1 A:HIS176 3.1 42.2 1.0
CG A:HIS176 3.2 39.3 1.0
OD1 A:ASP267 3.4 34.0 1.0
CB A:HIS176 3.6 31.1 1.0
N A:HIS176 3.8 39.2 1.0
C04 A:TWM701 4.0 46.8 1.0
CB A:ASP174 4.2 28.0 1.0
CG1 A:VAL175 4.2 34.5 1.0
N A:VAL175 4.2 33.8 1.0
NE2 A:HIS176 4.3 38.0 1.0
NE2 A:HIS136 4.3 37.5 1.0
CA A:HIS176 4.3 34.9 1.0
CD2 A:HIS176 4.3 44.9 1.0
CB A:ASP267 4.3 42.6 1.0
CA A:GLY305 4.4 41.8 1.0
CE1 A:HIS136 4.6 32.8 1.0
NE2 A:HIS137 4.6 43.1 1.0
OH A:TYR307 4.7 53.0 1.0
N A:GLY305 4.7 45.2 1.0
C A:VAL175 4.7 41.4 1.0
C23 A:TWM701 4.7 47.9 1.0
CE2 A:TYR307 4.8 43.0 1.0
CA A:VAL175 4.9 41.2 1.0
C A:ASP174 4.9 40.4 1.0
CA A:ASP174 4.9 28.4 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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