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Potassium in PDB 6ufo: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One:
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 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One, PDB code: 6ufo 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) 28.84 / 2.68
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.850, 80.850, 247.025, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23.5

Other elements in 6ufo:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One 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 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One (pdb code 6ufo). 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 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One, PDB code: 6ufo:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6ufo

Go back to Potassium Binding Sites List in 6ufo
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One


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 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K706

b:36.2
occ:1.00
O A:ASP174 2.7 38.9 1.0
O A:HIS176 2.7 29.5 1.0
O A:TRP196 2.7 44.8 1.0
OG A:SER195 2.8 36.5 1.0
O A:ASP172 2.8 37.1 1.0
OD2 A:ASP172 2.8 36.0 1.0
CG A:ASP172 3.1 40.8 1.0
C A:ASP172 3.5 43.0 1.0
CB A:ASP172 3.6 34.9 1.0
C A:ASP174 3.6 39.8 1.0
OD1 A:ASP172 3.7 44.2 1.0
N A:ASP174 3.7 30.7 1.0
CB A:SER195 3.8 35.2 1.0
C A:HIS176 3.8 37.0 1.0
C A:TRP196 3.9 35.9 1.0
CA A:ASP174 4.0 30.9 1.0
CB A:ASP174 4.1 29.6 1.0
N A:TRP196 4.1 33.4 1.0
CA A:ASP172 4.2 36.2 1.0
CA A:SER195 4.2 38.6 1.0
C A:TRP173 4.3 41.2 1.0
N A:TRP173 4.3 39.7 1.0
CA A:HIS177 4.4 41.1 1.0
CB A:HIS197 4.4 35.2 1.0
C A:SER195 4.4 41.9 1.0
N A:GLY178 4.5 38.0 1.0
CA A:TRP173 4.5 37.5 1.0
N A:HIS177 4.5 38.5 1.0
N A:HIS176 4.5 35.4 1.0
ND1 A:HIS197 4.6 38.5 1.0
CE1 A:HIS136 4.6 37.7 1.0
CA A:TRP196 4.7 36.7 1.0
OH A:TYR193 4.7 36.3 1.0
N A:VAL175 4.7 35.5 1.0
CD1 A:TRP196 4.7 33.9 1.0
CA A:HIS197 4.8 35.9 1.0
N A:HIS197 4.8 32.1 1.0
CA A:HIS176 4.8 31.1 1.0
C A:VAL175 4.9 39.3 1.0
C A:HIS177 4.9 41.3 1.0
ND1 A:HIS136 4.9 35.7 1.0
OD2 A:ASP174 4.9 38.3 1.0
CG A:HIS197 5.0 39.7 1.0

Potassium binding site 2 out of 2 in 6ufo

Go back to Potassium Binding Sites List in 6ufo
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One


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 7-[(3-Aminopropyl)Amino]-1-Methoxyheptan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K707

b:42.3
occ:1.00
O A:PHE185 2.7 48.7 1.0
O A:VAL191 2.7 44.2 1.0
O A:HOH816 2.9 45.8 1.0
O A:HOH840 2.9 37.7 1.0
O A:PHE224 2.9 38.8 1.0
O A:ASP188 3.1 44.5 1.0
C A:PHE224 3.5 42.8 1.0
CB A:PHE224 3.6 35.9 1.0
C A:PHE185 3.8 42.1 1.0
C A:VAL191 3.9 44.7 1.0
CB A:PHE185 4.0 39.7 1.0
C A:ASP188 4.2 47.1 1.0
CA A:PHE224 4.2 46.5 1.0
N A:ASN225 4.3 42.4 1.0
N A:TYR193 4.4 39.8 1.0
O A:GLY221 4.5 49.4 1.0
CA A:PHE185 4.5 41.4 1.0
CB A:ASN225 4.6 36.0 1.0
CA A:LEU192 4.6 38.9 1.0
N A:ASP188 4.6 44.1 1.0
CA A:ASN225 4.6 37.5 1.0
N A:LEU192 4.7 37.8 1.0
O A:GLU186 4.8 43.8 1.0
N A:GLU186 4.8 42.9 1.0
CA A:ASP188 4.8 42.0 1.0
C A:GLU186 4.9 48.0 1.0
CB A:TYR193 4.9 31.2 1.0
CA A:GLU186 4.9 38.6 1.0
CG A:PHE224 4.9 42.5 1.0
CA A:VAL191 4.9 40.7 1.0
OD1 A:ASN225 5.0 33.9 1.0
C A:LEU192 5.0 41.0 1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies For Blocking Polyamine Deacetylation. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31746596
DOI: 10.1021/ACS.BIOCHEM.9B00906
Page generated: Mon Dec 14 01:47:06 2020

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