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Potassium in PDB 7kuv: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Acetate

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Acetate

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Acetate:
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 Acetate, PDB code: 7kuv 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) 69.70 / 2.15
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.48, 80.48, 245.463, 90, 90, 120
R / Rfree (%) 18.5 / 21.8

Other elements in 7kuv:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Acetate 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 Acetate (pdb code 7kuv). 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 Acetate, PDB code: 7kuv:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7kuv

Go back to Potassium Binding Sites List in 7kuv
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Acetate


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 Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K705

b:25.0
occ:1.00
O A:TRP196 2.6 25.3 1.0
O A:ASP174 2.6 22.8 1.0
O A:HIS176 2.7 24.0 1.0
O A:ASP172 2.8 27.0 1.0
OD2 A:ASP172 2.8 23.4 1.0
OG A:SER195 2.8 21.1 1.0
CG A:ASP172 3.2 27.2 1.0
C A:ASP172 3.5 29.2 1.0
C A:ASP174 3.5 27.6 1.0
C A:HIS176 3.7 25.7 1.0
OD1 A:ASP172 3.7 29.1 1.0
CB A:ASP172 3.7 25.5 1.0
C A:TRP196 3.8 29.2 1.0
N A:ASP174 3.9 23.2 1.0
CB A:SER195 3.9 24.0 1.0
N A:TRP196 4.0 28.2 1.0
CA A:ASP174 4.1 19.8 1.0
CB A:ASP174 4.2 21.5 1.0
CA A:ASP172 4.2 23.2 1.0
CA A:SER195 4.3 21.5 1.0
N A:TRP173 4.3 27.3 1.0
C A:TRP173 4.3 24.8 1.0
CB A:HIS197 4.3 20.3 1.0
CA A:HIS177 4.3 22.9 1.0
N A:HIS176 4.4 27.9 1.0
N A:HIS177 4.4 24.5 1.0
C A:SER195 4.5 34.0 1.0
CA A:TRP173 4.5 22.6 1.0
N A:GLY178 4.5 24.9 1.0
ND1 A:HIS197 4.5 25.5 1.0
CD1 A:TRP196 4.6 27.5 1.0
CA A:TRP196 4.6 27.1 1.0
N A:VAL175 4.6 27.5 1.0
CE1 A:HIS136 4.6 21.2 1.0
CA A:HIS197 4.7 23.5 1.0
C A:VAL175 4.7 32.9 1.0
CA A:HIS176 4.7 26.9 1.0
N A:HIS197 4.7 22.1 1.0
OH A:TYR193 4.7 25.8 1.0
C A:HIS177 4.8 24.3 1.0
ND1 A:HIS136 4.9 22.6 1.0
CG A:HIS197 4.9 28.4 1.0
CA A:VAL175 5.0 26.9 1.0
O A:TRP173 5.0 27.5 1.0

Potassium binding site 2 out of 2 in 7kuv

Go back to Potassium Binding Sites List in 7kuv
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Acetate


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 Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K706

b:29.3
occ:1.00
O A:VAL191 2.6 26.4 1.0
O A:PHE185 2.6 32.5 1.0
O A:HOH910 2.8 28.3 1.0
O A:HOH864 2.8 23.1 1.0
O A:PHE224 2.9 29.2 1.0
O A:ASP188 2.9 31.4 1.0
C A:PHE185 3.6 26.5 1.0
C A:PHE224 3.6 35.4 1.0
CB A:PHE185 3.7 27.3 1.0
CB A:PHE224 3.8 26.1 1.0
C A:VAL191 3.8 31.1 1.0
C A:ASP188 4.1 30.9 1.0
CA A:PHE185 4.3 27.1 1.0
CA A:PHE224 4.3 28.8 1.0
N A:ASN225 4.4 28.4 1.0
N A:TYR193 4.4 27.4 1.0
N A:ASP188 4.5 35.1 1.0
N A:GLU186 4.6 26.6 1.0
O A:GLU186 4.6 31.2 1.0
CA A:LEU192 4.6 32.9 1.0
N A:LEU192 4.7 26.6 1.0
CA A:ASP188 4.7 35.6 1.0
C A:GLU186 4.7 33.9 1.0
CA A:GLU186 4.7 36.0 1.0
CA A:ASN225 4.8 30.3 1.0
CB A:ASN225 4.8 29.1 1.0
CB A:TYR193 4.8 25.7 1.0
CB A:ASP188 4.8 33.2 1.0
CA A:VAL191 4.8 33.3 1.0
OD1 A:ASN225 4.8 28.3 1.0
CB A:VAL191 4.9 29.5 1.0
O A:GLY221 4.9 29.7 1.0
C A:LEU192 4.9 31.9 1.0
CG A:PHE185 5.0 29.4 1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. X-Ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33449614
DOI: 10.1021/ACS.BIOCHEM.0C00936
Page generated: Wed Mar 3 14:22:02 2021

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