Potassium in PDB 7kut: Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate):
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate), PDB code: 7kut 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) 60.50 / 2.05
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.248, 80.248, 245.96, 90, 90, 120
R / Rfree (%) 17.6 / 21.9

Other elements in 7kut:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate) 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 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate) (pdb code 7kut). 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 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate), PDB code: 7kut:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7kut

Go back to Potassium Binding Sites List in 7kut
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)


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 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K712

b:24.5
occ:1.00
 O A:ASP174 2.6 23.0 1.0
O A:TRP196 2.6 21.8 1.0
O A:HIS176 2.7 23.7 1.0
OG A:SER195 2.8 18.7 1.0
OD2 A:ASP172 2.8 21.1 1.0
O A:ASP172 2.9 24.2 1.0
CG A:ASP172 3.2 23.3 1.0
C A:ASP174 3.6 26.7 1.0
C A:ASP172 3.6 28.4 1.0
C A:HIS176 3.7 23.8 1.0
OD1 A:ASP172 3.7 26.0 1.0
CB A:ASP172 3.8 22.7 1.0
C A:TRP196 3.8 22.4 1.0
CB A:SER195 3.8 16.3 1.0
N A:ASP174 3.9 22.9 1.0
N A:TRP196 4.1 25.7 1.0
CA A:ASP174 4.1 23.6 1.0
CB A:ASP174 4.1 20.5 1.0
CA A:SER195 4.2 20.1 1.0
CA A:HIS177 4.2 19.4 1.0
CB A:HIS197 4.3 21.9 1.0
C A:TRP173 4.3 23.8 1.0
CA A:ASP172 4.3 23.3 1.0
N A:HIS177 4.3 19.7 1.0
N A:TRP173 4.3 21.9 1.0
N A:HIS176 4.4 22.7 1.0
C A:SER195 4.5 27.1 1.0
CA A:TRP173 4.5 20.8 1.0
ND1 A:HIS197 4.5 22.7 1.0
N A:GLY178 4.5 24.1 1.0
CE1 A:HIS136 4.6 18.9 1.0
CA A:TRP196 4.6 20.6 1.0
CD1 A:TRP196 4.6 22.3 1.0
N A:VAL175 4.6 24.7 1.0
C A:HIS177 4.7 24.1 1.0
CA A:HIS176 4.7 24.3 1.0
CA A:HIS197 4.7 21.2 1.0
C A:VAL175 4.7 27.1 1.0
N A:HIS197 4.7 19.7 1.0
ND1 A:HIS136 4.8 23.1 1.0
OH A:TYR193 4.8 26.3 1.0
CG A:HIS197 4.9 24.4 1.0
CA A:VAL175 5.0 26.4 1.0
O A:TRP173 5.0 25.6 1.0

Potassium binding site 2 out of 2 in 7kut

Go back to Potassium Binding Sites List in 7kut
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)


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 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K713

b:40.5
occ:1.00
 O A:HOH1027 2.3 31.1 0.7
O A:VAL191 2.5 30.2 1.0
O A:PHE185 2.6 23.1 1.0
O A:HOH852 2.6 27.4 1.0
O A:ASP188 2.7 29.8 1.0
O A:PHE224 3.2 25.4 1.0
CB A:PHE224 3.6 26.1 1.0
C A:PHE185 3.6 23.5 1.0
C A:VAL191 3.7 30.4 1.0
O A:HOH864 3.7 25.7 0.9
C A:ASP188 3.7 31.6 1.0
CB A:PHE185 3.8 25.0 1.0
C A:PHE224 3.9 27.8 1.0
N A:ASP188 4.2 33.2 1.0
CA A:PHE185 4.3 20.2 1.0
CA A:PHE224 4.3 26.9 1.0
CA A:ASP188 4.4 29.3 1.0
CB A:ASP188 4.5 32.9 1.0
CA A:VAL191 4.5 26.0 1.0
N A:LEU192 4.6 28.6 1.0
N A:GLU186 4.6 24.1 1.0
N A:VAL191 4.6 27.6 1.0
CB A:VAL191 4.6 27.4 1.0
O A:GLU186 4.6 28.3 1.0
CA A:LEU192 4.6 30.2 1.0
C A:GLU186 4.7 32.0 1.0
N A:ASN225 4.7 26.6 1.0
N A:TYR193 4.7 23.3 1.0
N A:PRO189 4.7 28.9 1.0
O A:GLY221 4.8 29.2 1.0
CG A:PHE224 4.8 27.1 1.0
CA A:GLU186 4.8 29.9 1.0
CA A:PRO189 4.9 28.8 1.0
CG1 A:VAL191 5.0 24.3 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 14:22:01 2021

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