Atomistry » Potassium » PDB 5sc8-5u3q » 5td7
Atomistry »
  Potassium »
    PDB 5sc8-5u3q »
      5td7 »

Potassium in PDB 5td7: Crystal Structure of Histone Deacetylase 10

Protein crystallography data

The structure of Crystal Structure of Histone Deacetylase 10, PDB code: 5td7 was solved by Y.Hai, S.A.Shinsky, N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.51 / 2.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.449, 80.449, 243.037, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 22.7

Other elements in 5td7:

The structure of Crystal Structure of Histone Deacetylase 10 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Histone Deacetylase 10 (pdb code 5td7). 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 Histone Deacetylase 10, PDB code: 5td7:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 5td7

Go back to Potassium Binding Sites List in 5td7
Potassium binding site 1 out of 2 in the Crystal Structure of Histone Deacetylase 10


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 Histone Deacetylase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K702

b:46.3
occ:1.00
O A:ASP174 2.6 41.7 1.0
O A:HIS176 2.6 36.0 1.0
O A:ASP172 2.7 45.3 1.0
O A:TRP196 2.7 55.2 1.0
OD2 A:ASP172 2.8 39.4 1.0
OG A:SER195 2.8 39.5 1.0
CG A:ASP172 3.1 46.5 1.0
C A:ASP172 3.5 47.8 1.0
C A:ASP174 3.6 43.6 1.0
OD1 A:ASP172 3.7 46.1 1.0
C A:HIS176 3.7 41.9 1.0
CB A:ASP172 3.7 33.1 1.0
CB A:SER195 3.8 37.8 1.0
N A:ASP174 3.8 35.3 1.0
C A:TRP196 3.9 40.0 1.0
N A:TRP196 4.1 41.9 1.0
CA A:ASP174 4.1 39.0 1.0
CA A:SER195 4.2 42.5 1.0
CB A:ASP174 4.2 31.0 1.0
CA A:ASP172 4.2 33.1 1.0
CA A:HIS177 4.2 43.1 1.0
CB A:HIS197 4.3 39.8 1.0
C A:TRP173 4.3 47.0 1.0
N A:TRP173 4.3 44.7 1.0
N A:HIS177 4.4 37.2 1.0
C A:SER195 4.4 49.7 1.0
ND1 A:HIS197 4.5 47.0 1.0
CA A:TRP173 4.5 42.5 1.0
N A:HIS176 4.5 41.2 1.0
N A:GLY178 4.5 38.5 1.0
OH A:TYR193 4.6 38.8 1.0
CA A:TRP196 4.6 32.6 1.0
CD1 A:TRP196 4.7 39.1 1.0
CE1 A:HIS136 4.7 41.6 1.0
N A:VAL175 4.7 48.2 1.0
ND1 A:HIS136 4.7 46.9 1.0
CA A:HIS197 4.7 40.9 1.0
CA A:HIS176 4.7 31.8 1.0
C A:HIS177 4.8 42.8 1.0
C A:VAL175 4.8 43.5 1.0
N A:HIS197 4.8 28.1 1.0
CG A:HIS197 4.9 41.7 1.0
OD2 A:ASP174 5.0 43.0 1.0

Potassium binding site 2 out of 2 in 5td7

Go back to Potassium Binding Sites List in 5td7
Potassium binding site 2 out of 2 in the Crystal Structure of Histone Deacetylase 10


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 Histone Deacetylase 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K703

b:54.5
occ:1.00
O A:PHE185 2.6 42.9 1.0
O A:VAL191 2.7 55.0 1.0
O A:HOH812 2.8 46.6 1.0
O A:PHE224 2.9 48.9 1.0
O A:ASP188 2.9 61.4 1.0
C A:PHE224 3.6 47.5 1.0
C A:PHE185 3.7 54.9 1.0
CB A:PHE224 3.7 49.8 1.0
CB A:PHE185 3.9 48.4 1.0
C A:VAL191 3.9 51.6 1.0
C A:ASP188 4.0 54.5 1.0
CA A:PHE224 4.3 44.0 1.0
N A:ASN225 4.4 48.6 1.0
O A:GLU186 4.4 66.6 1.0
O A:GLY221 4.4 75.1 1.0
CA A:PHE185 4.4 49.0 1.0
N A:ASP188 4.5 61.2 1.0
N A:TYR193 4.6 38.8 1.0
CB A:ASN225 4.6 35.6 1.0
N A:GLU186 4.6 55.3 1.0
CA A:ASP188 4.7 49.4 1.0
CA A:LEU192 4.7 45.3 1.0
C A:GLU186 4.7 64.4 1.0
N A:LEU192 4.7 48.1 1.0
CA A:ASN225 4.7 33.1 1.0
CA A:GLU186 4.8 49.5 1.0
CB A:ASP188 4.8 58.4 1.0
CA A:VAL191 4.8 49.1 1.0
CB A:VAL191 4.9 56.3 1.0
N A:VAL191 4.9 46.8 1.0
OD1 A:ASN225 5.0 49.9 1.0

Reference:

Y.Hai, S.A.Shinsky, N.J.Porter, D.W.Christianson. Histone Deacetylase 10 Structure and Molecular Function As A Polyamine Deacetylase. Nat Commun V. 8 15368 2017.
ISSN: ESSN 2041-1723
PubMed: 28516954
DOI: 10.1038/NCOMMS15368
Page generated: Mon Aug 12 14:34:45 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy