Potassium in PDB 7kur: Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine

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

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine:
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 N-Acetylputrescine, PDB code: 7kur 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) 69.77 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.56, 80.56, 245.71, 90, 90, 120
R / Rfree (%) 19.1 / 21.7

Other elements in 7kur:

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

Zinc (Zn) 1 atom
Sodium (Na) 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 N-Acetylputrescine (pdb code 7kur). 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 N-Acetylputrescine, PDB code: 7kur:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7kur

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


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 N-Acetylputrescine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K704

b:26.9
occ:1.00
O A:ASP174 2.6 26.9 1.0
O A:TRP196 2.7 27.5 1.0
O A:HIS176 2.7 27.8 1.0
OD2 A:ASP172 2.7 24.3 1.0
O A:ASP172 2.8 27.9 1.0
OG A:SER195 2.8 22.4 1.0
CG A:ASP172 3.1 27.9 1.0
C A:ASP172 3.5 31.8 1.0
C A:ASP174 3.6 31.4 1.0
OD1 A:ASP172 3.7 32.7 1.0
C A:HIS176 3.7 28.6 1.0
CB A:ASP172 3.8 24.6 1.0
C A:TRP196 3.8 29.1 1.0
N A:ASP174 3.9 25.9 1.0
CB A:SER195 3.9 24.1 1.0
N A:TRP196 4.0 26.4 1.0
CA A:ASP174 4.1 26.0 1.0
CB A:ASP174 4.1 23.5 1.0
CA A:SER195 4.2 22.9 1.0
CA A:ASP172 4.3 24.0 1.0
N A:TRP173 4.3 32.5 1.0
C A:TRP173 4.3 27.0 1.0
CA A:HIS177 4.4 26.1 1.0
CB A:HIS197 4.4 24.5 1.0
N A:HIS176 4.4 29.1 1.0
C A:SER195 4.5 31.1 1.0
N A:HIS177 4.5 23.7 1.0
CA A:TRP173 4.5 24.9 1.0
N A:GLY178 4.5 25.9 1.0
ND1 A:HIS197 4.5 25.4 1.0
CA A:TRP196 4.6 26.1 1.0
CD1 A:TRP196 4.6 27.2 1.0
N A:VAL175 4.6 27.9 1.0
CE1 A:HIS136 4.6 25.6 1.0
C A:VAL175 4.7 31.6 1.0
CA A:HIS176 4.7 25.9 1.0
OH A:TYR193 4.8 29.0 1.0
CA A:HIS197 4.8 25.0 1.0
N A:HIS197 4.8 25.4 1.0
C A:HIS177 4.9 23.4 1.0
ND1 A:HIS136 4.9 24.3 1.0
OD2 A:ASP174 5.0 27.0 1.0
CA A:VAL175 5.0 29.5 1.0
CG A:HIS197 5.0 25.0 1.0

Potassium binding site 2 out of 2 in 7kur

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


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 N-Acetylputrescine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K705

b:44.6
occ:1.00
O A:HOH951 2.3 35.3 1.0
O A:ASP188 2.4 34.5 1.0
O A:VAL191 2.4 34.1 1.0
O A:PHE185 2.5 28.1 1.0
O A:HOH876 2.6 29.8 1.0
O A:PHE224 3.4 32.2 1.0
C A:ASP188 3.5 37.1 1.0
CB A:PHE224 3.6 27.4 1.0
C A:PHE185 3.6 26.2 1.0
C A:VAL191 3.6 38.3 1.0
CB A:PHE185 3.7 24.6 1.0
O A:HOH825 3.9 28.5 1.0
C A:PHE224 4.0 32.8 1.0
N A:ASP188 4.0 34.6 1.0
CA A:ASP188 4.2 35.9 1.0
CA A:PHE185 4.3 21.2 1.0
CB A:ASP188 4.4 37.4 1.0
CA A:PHE224 4.4 30.5 1.0
CA A:VAL191 4.4 33.5 1.0
CB A:VAL191 4.5 32.5 1.0
N A:VAL191 4.5 29.4 1.0
N A:PRO189 4.5 32.6 1.0
N A:GLU186 4.6 25.8 1.0
O A:GLU186 4.6 33.2 1.0
C A:GLU186 4.6 34.9 1.0
CA A:GLU186 4.6 35.5 1.0
N A:LEU192 4.6 32.3 1.0
CA A:PRO189 4.7 33.5 1.0
CG A:PHE224 4.7 30.0 1.0
CA A:LEU192 4.7 33.5 1.0
O A:GLY221 4.8 30.0 1.0
N A:ASN225 4.9 28.2 1.0
N A:TYR193 4.9 29.3 1.0
CG1 A:VAL191 5.0 28.8 1.0
CG A:PHE185 5.0 28.0 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 14:20:42 2021

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