Atomistry » Potassium » PDB 7k5h-7lo2 » 7kus
Atomistry »
  Potassium »
    PDB 7k5h-7lo2 »
      7kus »

Potassium in PDB 7kus: Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate)

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate)

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (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 N8-Acetylspermidine (Tetrahedral Intermediate), PDB code: 7kus 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) 60.60 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.489, 80.489, 245.308, 90, 90, 120
R / Rfree (%) 17.5 / 21.2

Other elements in 7kus:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate) 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 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate) (pdb code 7kus). 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 N8-Acetylspermidine (Tetrahedral Intermediate), PDB code: 7kus:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7kus

Go back to Potassium Binding Sites List in 7kus
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (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 N8-Acetylspermidine (Tetrahedral Intermediate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K706

b:26.2
occ:1.00
 O A:TRP196 2.6 24.6 1.0
O A:ASP174 2.6 27.2 1.0
O A:HIS176 2.7 24.8 1.0
OG A:SER195 2.7 23.4 1.0
OD2 A:ASP172 2.8 24.4 1.0
O A:ASP172 2.9 26.0 1.0
CG A:ASP172 3.2 27.2 1.0
C A:ASP174 3.6 28.5 1.0
C A:ASP172 3.6 28.3 1.0
OD1 A:ASP172 3.7 32.2 1.0
C A:HIS176 3.7 27.1 1.0
CB A:ASP172 3.8 24.5 1.0
C A:TRP196 3.8 25.8 1.0
CB A:SER195 3.8 21.7 1.0
N A:ASP174 3.9 25.1 1.0
N A:TRP196 4.1 29.1 1.0
CA A:ASP174 4.1 26.3 1.0
CB A:ASP174 4.1 23.7 1.0
CA A:SER195 4.2 22.7 1.0
CA A:HIS177 4.3 21.6 1.0
CB A:HIS197 4.3 23.8 1.0
CA A:ASP172 4.3 24.5 1.0
C A:TRP173 4.3 24.0 1.0
N A:HIS177 4.3 22.8 1.0
N A:TRP173 4.4 24.6 1.0
N A:HIS176 4.4 25.2 1.0
ND1 A:HIS197 4.5 25.7 1.0
C A:SER195 4.5 28.4 1.0
N A:GLY178 4.5 26.9 1.0
CA A:TRP173 4.5 23.4 1.0
CA A:TRP196 4.6 25.9 1.0
CD1 A:TRP196 4.6 23.8 1.0
N A:VAL175 4.6 25.3 1.0
CE1 A:HIS136 4.6 25.9 1.0
C A:HIS177 4.7 27.3 1.0
CA A:HIS197 4.7 24.8 1.0
CA A:HIS176 4.7 25.2 1.0
C A:VAL175 4.7 29.4 1.0
N A:HIS197 4.7 22.4 1.0
OH A:TYR193 4.7 27.4 1.0
ND1 A:HIS136 4.8 26.6 1.0
CG A:HIS197 4.9 26.0 1.0
CA A:VAL175 5.0 26.9 1.0

Potassium binding site 2 out of 2 in 7kus

Go back to Potassium Binding Sites List in 7kus
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (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 N8-Acetylspermidine (Tetrahedral Intermediate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K707

b:44.5
occ:1.00
 O A:HOH972 2.3 37.8 1.0
O A:VAL191 2.4 29.5 1.0
O A:ASP188 2.5 30.6 1.0
O A:HOH858 2.6 32.1 1.0
O A:PHE185 2.6 29.3 1.0
O A:PHE224 3.3 30.8 1.0
CB A:PHE224 3.5 27.6 1.0
C A:ASP188 3.6 33.1 1.0
C A:VAL191 3.6 34.1 1.0
C A:PHE185 3.6 27.4 1.0
O A:HOH947 3.8 30.3 1.0
CB A:PHE185 3.8 32.2 1.0
C A:PHE224 3.9 32.6 1.0
N A:ASP188 4.1 35.7 1.0
CA A:ASP188 4.3 31.9 1.0
CA A:PHE224 4.3 31.7 1.0
CA A:PHE185 4.3 28.2 1.0
CB A:ASP188 4.5 35.8 1.0
CA A:VAL191 4.5 29.8 1.0
N A:VAL191 4.5 29.2 1.0
CB A:VAL191 4.5 31.0 1.0
O A:GLU186 4.6 31.1 1.0
N A:PRO189 4.6 30.8 1.0
N A:LEU192 4.6 29.2 1.0
N A:GLU186 4.6 28.1 1.0
CG A:PHE224 4.7 29.2 1.0
C A:GLU186 4.7 34.5 1.0
O A:GLY221 4.7 31.7 1.0
CA A:LEU192 4.7 32.2 1.0
CA A:PRO189 4.7 31.2 1.0
N A:ASN225 4.8 29.4 1.0
CA A:GLU186 4.8 34.9 1.0
N A:TYR193 4.9 24.9 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: Mon Aug 12 19:17:40 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy