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Potassium 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:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dimethylaminoethylindole Phenylhydroxamate Inhibitor, PDB code: 6wdw:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6wdw

Go back to Potassium Binding Sites List in 6wdw
Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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:K706

b:27.4
occ:1.00
O A:TRP196 2.6 27.3 1.0
O A:HIS176 2.7 26.7 1.0
O A:ASP174 2.7 28.5 1.0
OD2 A:ASP172 2.7 24.0 1.0
OG A:SER195 2.8 24.1 1.0
O A:ASP172 2.9 29.5 1.0
CG A:ASP172 3.2 26.7 1.0
C A:ASP174 3.5 30.3 1.0
C A:ASP172 3.6 29.5 1.0
OD1 A:ASP172 3.7 26.7 1.0
C A:HIS176 3.8 27.9 1.0
N A:ASP174 3.8 23.2 1.0
C A:TRP196 3.8 28.9 1.0
CB A:SER195 3.8 26.1 1.0
CB A:ASP172 3.8 22.9 1.0
CA A:ASP174 4.0 24.1 1.0
N A:TRP196 4.1 28.6 1.0
CB A:ASP174 4.1 24.4 1.0
CA A:SER195 4.3 26.5 1.0
C A:TRP173 4.3 28.1 1.0
N A:TRP173 4.3 26.5 1.0
CA A:ASP172 4.3 24.7 1.0
CB A:HIS197 4.3 24.3 1.0
CA A:HIS177 4.4 29.0 1.0
N A:HIS176 4.4 31.6 1.0
ND1 A:HIS197 4.4 29.4 1.0
C A:SER195 4.5 33.6 1.0
CA A:TRP173 4.5 23.2 1.0
N A:GLY178 4.5 27.4 1.0
N A:HIS177 4.5 25.3 1.0
N A:VAL175 4.6 30.8 1.0
CD1 A:TRP196 4.6 26.6 1.0
CA A:TRP196 4.6 23.7 1.0
CE1 A:HIS136 4.7 26.3 1.0
CA A:HIS197 4.7 23.7 1.0
C A:VAL175 4.7 31.9 1.0
CA A:HIS176 4.7 28.9 1.0
N A:HIS197 4.7 25.6 1.0
OH A:TYR193 4.7 26.3 1.0
ND1 A:HIS136 4.9 28.0 1.0
C A:HIS177 4.9 25.7 1.0
CG A:HIS197 4.9 30.1 1.0
CA A:VAL175 4.9 31.1 1.0

Potassium binding site 2 out of 2 in 6wdw

Go back to Potassium Binding Sites List in 6wdw
Potassium binding site 2 out of 2 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 Potassium with other atoms in the K binding site number 2 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:K707

b:30.3
occ:1.00
O A:VAL191 2.6 31.6 1.0
O A:PHE185 2.7 37.2 1.0
O A:HOH820 2.8 29.3 1.0
O A:HOH906 2.8 31.6 1.0
O A:PHE224 2.9 32.6 1.0
O A:ASP188 3.0 38.4 1.0
CB A:PHE185 3.6 30.6 1.0
C A:PHE185 3.6 35.9 1.0
C A:PHE224 3.6 33.5 1.0
CB A:PHE224 3.7 30.9 1.0
C A:VAL191 3.9 33.2 1.0
C A:ASP188 4.1 35.9 1.0
CA A:PHE185 4.2 30.5 1.0
CA A:PHE224 4.3 35.8 1.0
N A:ASN225 4.4 31.5 1.0
N A:TYR193 4.4 26.8 1.0
N A:ASP188 4.5 41.5 1.0
N A:GLU186 4.6 30.7 1.0
O A:GLU186 4.6 35.7 1.0
CA A:LEU192 4.6 33.3 1.0
CA A:ASP188 4.7 36.3 1.0
N A:LEU192 4.7 29.8 1.0
C A:GLU186 4.8 38.5 1.0
CA A:ASN225 4.8 33.9 1.0
CA A:GLU186 4.8 37.8 1.0
CB A:TYR193 4.8 24.4 1.0
CB A:ASP188 4.8 35.8 1.0
CA A:VAL191 4.9 32.2 1.0
CG A:PHE185 4.9 32.6 1.0
CB A:ASN225 4.9 34.2 1.0
CB A:VAL191 4.9 30.0 1.0
O A:GLY221 4.9 36.7 1.0
OD1 A:ASN225 4.9 32.3 1.0
C A:LEU192 5.0 36.5 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: Mon Dec 14 02:17:40 2020

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