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Potassium in PDB 6uij: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} 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 S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate, PDB code: 6uij 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) 45.83 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.780, 80.780, 242.602, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 24.9

Other elements in 6uij:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} 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 S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate (pdb code 6uij). 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 S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate, PDB code: 6uij:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6uij

Go back to Potassium Binding Sites List in 6uij
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} 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 S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K705

b:54.2
occ:1.00
O A:ASP174 2.5 51.2 1.0
O A:TRP196 2.6 61.3 1.0
O A:HIS176 2.6 49.6 1.0
O A:ASP172 2.8 52.8 1.0
OG A:SER195 2.9 55.3 1.0
OD2 A:ASP172 3.0 44.5 1.0
CG A:ASP172 3.3 50.9 1.0
C A:ASP174 3.4 55.0 1.0
C A:TRP196 3.6 52.5 1.0
C A:HIS176 3.7 52.4 1.0
C A:ASP172 3.7 49.2 1.0
OD1 A:ASP172 3.7 55.9 1.0
CB A:ASP172 3.8 43.3 1.0
N A:ASP174 3.9 41.3 1.0
N A:TRP196 3.9 47.4 1.0
CB A:SER195 3.9 51.9 1.0
CA A:ASP174 4.0 48.6 1.0
CB A:HIS197 4.1 46.8 1.0
CB A:ASP174 4.1 50.7 1.0
CA A:SER195 4.2 50.1 1.0
CA A:HIS177 4.3 59.7 1.0
C A:SER195 4.3 49.7 1.0
N A:HIS176 4.4 49.9 1.0
CA A:ASP172 4.4 47.6 1.0
C A:TRP173 4.4 45.7 1.0
N A:HIS177 4.4 60.4 1.0
N A:VAL175 4.4 54.6 1.0
ND1 A:HIS197 4.4 54.9 1.0
CA A:TRP196 4.5 46.6 1.0
N A:TRP173 4.5 48.5 1.0
CA A:HIS197 4.5 48.2 1.0
N A:GLY178 4.5 53.7 1.0
N A:HIS197 4.5 48.1 1.0
CD1 A:TRP196 4.6 49.0 1.0
C A:VAL175 4.6 53.3 1.0
CA A:TRP173 4.6 47.9 1.0
CA A:HIS176 4.7 46.8 1.0
CG A:HIS197 4.7 54.2 1.0
CA A:VAL175 4.7 51.1 1.0
OH A:TYR193 4.8 49.6 1.0
C A:HIS177 4.9 56.4 1.0
ND1 A:HIS136 4.9 46.3 1.0
CE1 A:HIS136 5.0 49.2 1.0

Potassium binding site 2 out of 2 in 6uij

Go back to Potassium Binding Sites List in 6uij
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with S-{5-[(3-Aminopropyl)Amino]Pentyl} 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 S-{5-[(3-Aminopropyl)Amino]Pentyl} Thioacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K706

b:76.5
occ:1.00
O A:PHE185 2.7 60.9 1.0
O A:VAL191 2.9 64.7 1.0
O A:HOH816 2.9 49.3 1.0
O A:PHE224 3.0 59.0 1.0
O A:ASP188 3.1 68.5 1.0
C A:PHE224 3.6 62.5 1.0
C A:PHE185 3.7 65.7 1.0
CB A:PHE224 3.8 66.8 1.0
CB A:PHE185 3.8 53.5 1.0
C A:VAL191 4.1 60.4 1.0
N A:ASN225 4.1 60.7 1.0
O A:GLU186 4.2 62.5 1.0
C A:ASP188 4.3 69.3 1.0
CA A:PHE224 4.3 65.4 1.0
CA A:PHE185 4.4 59.9 1.0
N A:TYR193 4.4 56.4 1.0
CB A:ASN225 4.5 45.7 1.0
CA A:ASN225 4.5 52.5 1.0
N A:GLU186 4.6 65.5 1.0
CA A:GLU186 4.7 60.5 1.0
C A:GLU186 4.7 65.4 1.0
CB A:TYR193 4.7 54.9 1.0
N A:ASP188 4.7 70.6 1.0
O A:GLY221 4.8 62.4 1.0
CA A:LEU192 4.8 56.9 1.0
CA A:ASP188 4.9 70.5 1.0
N A:LEU192 4.9 55.4 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 01:48:48 2020

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