Potassium in PDB 6uim: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-{[(3-Aminopropyl)Amino]-2-Oxoheptyl} Thioacetate

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-{[(3-Aminopropyl)Amino]-2-Oxoheptyl} Thioacetate

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-{[(3-Aminopropyl)Amino]-2-Oxoheptyl} Thioacetate:
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]-2-Oxoheptyl} Thioacetate, PDB code: 6uim 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) 45.73 / 2.75
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.871, 80.871, 241.540, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 27.6

Other elements in 6uim:

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

Potassium binding site 1 out of 2 in 6uim

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


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]-2-Oxoheptyl} Thioacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K705

b:58.1
occ:1.00
 O A:ASP174 2.6 46.8 1.0
O A:HIS176 2.6 49.9 1.0
O A:TRP196 2.7 64.9 1.0
OG A:SER195 2.9 54.8 1.0
OD2 A:ASP172 2.9 49.0 1.0
O A:ASP172 2.9 61.6 1.0
CG A:ASP172 3.3 51.6 1.0
C A:ASP174 3.4 58.1 1.0
C A:HIS176 3.6 52.7 1.0
OD1 A:ASP172 3.8 54.8 1.0
C A:ASP172 3.8 52.3 1.0
N A:ASP174 3.8 44.8 1.0
C A:TRP196 3.8 54.2 1.0
CA A:ASP174 3.9 47.6 1.0
CB A:ASP174 3.9 45.6 1.0
CB A:ASP172 3.9 43.7 1.0
CB A:SER195 4.0 53.7 1.0
CB A:HIS197 4.0 45.6 1.0
N A:HIS176 4.1 45.8 1.0
CA A:HIS177 4.2 60.4 1.0
N A:HIS177 4.3 64.7 1.0
N A:VAL175 4.3 55.8 1.0
N A:TRP196 4.4 53.3 1.0
ND1 A:HIS197 4.4 58.4 1.0
N A:GLY178 4.4 53.9 1.0
CA A:SER195 4.4 54.4 1.0
C A:TRP173 4.5 50.3 1.0
CA A:HIS176 4.5 46.0 1.0
CA A:HIS197 4.5 53.2 1.0
C A:VAL175 4.5 57.0 1.0
CA A:ASP172 4.5 46.1 1.0
C A:SER195 4.6 54.7 1.0
N A:HIS197 4.6 50.5 1.0
N A:TRP173 4.6 39.6 1.0
CG A:HIS197 4.7 59.5 1.0
CA A:VAL175 4.7 55.9 1.0
OH A:TYR193 4.7 50.8 1.0
CE1 A:HIS136 4.8 47.1 1.0
C A:HIS177 4.8 57.8 1.0
CA A:TRP173 4.8 45.2 1.0
CA A:TRP196 4.8 50.0 1.0
ND1 A:HIS136 4.8 49.3 1.0
CD1 A:TRP196 4.8 51.7 1.0

Potassium binding site 2 out of 2 in 6uim

Go back to Potassium Binding Sites List in 6uim
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 7-{[(3-Aminopropyl)Amino]-2-Oxoheptyl} Thioacetate


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]-2-Oxoheptyl} Thioacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K706

b:71.3
occ:1.00
 O A:PHE185 2.8 59.8 1.0
O A:VAL191 2.8 56.9 1.0
O A:HOH810 3.0 42.0 1.0
O A:PHE224 3.0 52.3 1.0
O A:ASP188 3.1 67.0 1.0
O A:HOH801 3.1 66.8 1.0
C A:PHE224 3.4 64.5 1.0
CB A:PHE224 3.6 70.6 1.0
C A:PHE185 3.9 64.3 1.0
N A:ASN225 4.0 57.0 1.0
C A:VAL191 4.1 60.0 1.0
CB A:PHE185 4.1 53.5 1.0
CA A:PHE224 4.1 68.4 1.0
C A:ASP188 4.2 66.8 1.0
N A:TYR193 4.3 56.1 1.0
O A:GLU186 4.4 60.8 1.0
CA A:ASN225 4.4 49.8 1.0
CB A:ASN225 4.4 39.5 1.0
O A:GLY221 4.5 61.4 1.0
CA A:PHE185 4.6 55.1 1.0
CA A:LEU192 4.6 57.4 1.0
CB A:TYR193 4.7 61.0 1.0
N A:LEU192 4.8 53.9 1.0
N A:GLU186 4.9 64.9 1.0
N A:ASP188 4.9 65.9 1.0
C A:GLU186 4.9 60.7 1.0
CG A:PHE224 4.9 64.4 1.0
N A:PHE224 4.9 57.8 1.0
CA A:GLU186 4.9 63.9 1.0
OD1 A:ASN225 4.9 65.0 1.0
C A:LEU192 5.0 53.3 1.0
CA A:ASP188 5.0 65.4 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 01:49:20 2020

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