Potassium in PDB 7kuq: Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine, PDB code: 7kuq 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) 60.85 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.509, 80.509, 249.38, 90, 90, 120
R / Rfree (%) 20.5 / 24.7

Other elements in 7kuq:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine also contains other interesting chemical elements:

Sodium (Na) 1 atom
Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine (pdb code 7kuq). 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 Y307F Mutant in Complex with N8-Acetylspermidine, PDB code: 7kuq:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7kuq

Go back to Potassium Binding Sites List in 7kuq
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine


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 Y307F Mutant in Complex with N8-Acetylspermidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K703

b:24.2
occ:1.00
O A:TRP196 2.7 23.6 1.0
O A:HIS176 2.7 25.8 1.0
O A:ASP174 2.7 22.9 1.0
OD2 A:ASP172 2.7 19.6 1.0
OG A:SER195 2.8 18.0 1.0
O A:ASP172 2.9 27.4 1.0
CG A:ASP172 3.1 24.6 1.0
C A:ASP172 3.5 28.2 1.0
C A:ASP174 3.6 25.9 1.0
OD1 A:ASP172 3.7 26.5 1.0
CB A:ASP172 3.7 21.3 1.0
C A:HIS176 3.8 25.0 1.0
N A:ASP174 3.8 20.6 1.0
CB A:SER195 3.8 19.0 1.0
C A:TRP196 3.9 23.5 1.0
N A:TRP196 4.1 25.4 1.0
CA A:ASP174 4.1 23.9 1.0
CB A:ASP174 4.1 24.8 1.0
CA A:ASP172 4.2 21.0 1.0
N A:TRP173 4.2 24.6 1.0
CA A:SER195 4.3 18.5 1.0
C A:TRP173 4.3 20.7 1.0
CA A:HIS177 4.4 25.8 1.0
N A:HIS176 4.5 29.3 1.0
CA A:TRP173 4.5 21.3 1.0
CB A:HIS197 4.5 22.1 1.0
ND1 A:HIS197 4.5 19.2 1.0
N A:HIS177 4.5 24.5 1.0
N A:GLY178 4.5 25.1 1.0
C A:SER195 4.5 28.7 1.0
CD1 A:TRP196 4.5 27.4 1.0
CA A:TRP196 4.7 20.5 1.0
N A:VAL175 4.7 27.8 1.0
CE1 A:HIS136 4.7 21.0 1.0
C A:VAL175 4.7 29.7 1.0
OH A:TYR193 4.8 24.0 1.0
CA A:HIS176 4.8 24.8 1.0
CA A:HIS197 4.8 20.4 1.0
N A:HIS197 4.8 21.4 1.0
C A:HIS177 4.8 25.5 1.0
ND1 A:HIS136 4.9 22.5 1.0
OD2 A:ASP174 4.9 20.0 1.0
CG A:HIS197 5.0 20.9 1.0
CA A:VAL175 5.0 28.2 1.0

Potassium binding site 2 out of 2 in 7kuq

Go back to Potassium Binding Sites List in 7kuq
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine


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 Y307F Mutant in Complex with N8-Acetylspermidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K704

b:43.9
occ:1.00
O A:HOH908 2.3 26.4 1.0
O A:ASP188 2.4 29.8 1.0
O A:PHE185 2.4 23.3 1.0
O A:HOH873 2.5 26.1 1.0
O A:VAL191 2.6 30.6 1.0
C A:ASP188 3.4 30.6 1.0
C A:PHE185 3.4 27.4 1.0
CB A:PHE185 3.7 25.7 1.0
O A:PHE224 3.7 24.2 1.0
C A:VAL191 3.8 29.9 1.0
CB A:PHE224 3.8 27.5 1.0
N A:ASP188 3.9 31.9 1.0
O A:HOH899 3.9 24.4 1.0
CA A:ASP188 4.0 32.9 1.0
CA A:PHE185 4.1 19.6 1.0
CB A:ASP188 4.2 26.1 1.0
C A:PHE224 4.3 25.9 1.0
O A:GLU186 4.4 32.9 1.0
N A:GLU186 4.4 26.0 1.0
CB A:VAL191 4.4 32.5 1.0
N A:PRO189 4.5 30.3 1.0
CA A:VAL191 4.5 32.2 1.0
N A:VAL191 4.5 29.6 1.0
C A:GLU186 4.5 35.2 1.0
CA A:PHE224 4.7 27.8 1.0
CA A:PRO189 4.7 27.0 1.0
CA A:GLU186 4.8 29.6 1.0
O A:GLY221 4.8 30.2 1.0
N A:LEU192 4.8 28.8 1.0
C A:GLU187 4.9 36.5 1.0
CG A:PHE185 4.9 25.1 1.0
CG A:PHE224 5.0 23.5 1.0
CG1 A:VAL191 5.0 25.4 1.0
N A:GLU187 5.0 37.3 1.0
CA A:LEU192 5.0 30.1 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 14:20:43 2021

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