Atomistry » Potassium » PDB 3q9c-3rs8 » 3rqd
Atomistry »
  Potassium »
    PDB 3q9c-3rs8 »
      3rqd »

Potassium in PDB 3rqd: Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8

Enzymatic activity of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8

All present enzymatic activity of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8:
3.5.1.98;

Protein crystallography data

The structure of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8, PDB code: 3rqd was solved by K.E.Cole, D.P.Dowling, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.78 / 2.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.059, 88.302, 93.660, 90.00, 101.62, 90.00
R / Rfree (%) 20.2 / 24.5

Other elements in 3rqd:

The structure of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 (pdb code 3rqd). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8, PDB code: 3rqd:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3rqd

Go back to Potassium Binding Sites List in 3rqd
Potassium binding site 1 out of 4 in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:17.5
occ:1.00
 O A:LEU200 2.8 13.0 1.0
O A:HIS180 2.9 13.8 1.0
O A:ASP178 2.9 18.3 1.0
O A:ASP176 3.0 15.7 1.0
OD1 A:ASP176 3.1 24.2 1.0
OG A:SER199 3.1 25.3 1.0
C A:ASP176 3.6 19.0 1.0
CG A:ASP176 3.6 26.2 1.0
N A:ASP178 3.7 18.1 1.0
C A:ASP178 3.7 16.4 1.0
C A:LEU200 3.7 22.1 1.0
C A:HIS180 3.8 19.6 1.0
CB A:HIS201 3.8 17.9 1.0
CB A:ASP176 3.9 18.4 1.0
N A:LEU200 4.0 17.5 1.0
C A:LEU177 4.1 23.6 1.0
CB A:ASP178 4.1 16.7 1.0
CA A:ASP178 4.1 18.9 1.0
N A:LEU177 4.2 21.6 1.0
CB A:SER199 4.2 21.6 1.0
N A:GLY182 4.2 19.8 1.0
CA A:LEU177 4.3 18.0 1.0
CA A:HIS181 4.3 18.3 1.0
CA A:ASP176 4.4 18.2 1.0
ND1 A:HIS201 4.4 19.1 1.0
CA A:HIS201 4.4 18.2 1.0
CA A:SER199 4.4 23.1 1.0
N A:HIS181 4.4 15.6 1.0
N A:HIS180 4.4 16.0 1.0
OD2 A:ASP176 4.4 28.9 1.0
C A:SER199 4.5 17.1 1.0
N A:HIS201 4.5 19.5 1.0
O A:HOH503 4.5 20.4 1.0
CG A:HIS201 4.5 18.0 1.0
C A:LEU179 4.6 20.1 1.0
CA A:LEU200 4.6 22.7 1.0
C A:HIS181 4.6 26.9 1.0
O A:LEU177 4.7 17.4 1.0
CA A:HIS180 4.7 13.1 1.0
N A:LEU179 4.8 16.0 1.0
O A:LEU179 4.8 16.8 1.0
CE1 A:HIS142 4.9 21.4 1.0

Potassium binding site 2 out of 4 in 3rqd

Go back to Potassium Binding Sites List in 3rqd
Potassium binding site 2 out of 4 in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:24.9
occ:1.00
 O A:VAL195 2.8 23.9 1.0
O A:PHE189 2.9 21.6 1.0
O A:THR192 3.0 20.1 1.0
O A:HOH511 3.1 18.5 1.0
O A:HOH563 3.2 29.9 1.0
O A:TYR225 3.2 21.8 1.0
CB A:TYR225 3.6 25.9 1.0
C A:PHE189 3.7 23.5 1.0
C A:TYR225 3.8 26.3 1.0
C A:VAL195 4.0 23.6 1.0
CB A:PHE189 4.1 22.3 1.0
OG A:SER226 4.1 20.5 1.0
C A:THR192 4.1 27.2 1.0
CA A:TYR225 4.3 21.2 1.0
CA A:SER190 4.3 20.9 1.0
CA A:MET196 4.4 18.6 1.0
N A:SER190 4.4 23.4 1.0
N A:SER226 4.5 30.8 1.0
O A:GLY222 4.5 23.7 1.0
CG2 A:THR192 4.5 20.1 1.0
C A:SER190 4.5 31.5 1.0
CA A:PHE189 4.6 22.3 1.0
N A:THR197 4.6 27.8 1.0
N A:THR192 4.6 27.1 1.0
O A:SER190 4.7 21.9 1.0
N A:MET196 4.7 21.0 1.0
OG1 A:THR197 4.8 28.8 1.0
CA A:GLY222 4.8 22.5 1.0
CA A:THR192 4.9 26.9 1.0
C A:MET196 4.9 23.1 1.0
CG A:TYR225 4.9 33.8 1.0
CA A:SER226 5.0 21.5 1.0

Potassium binding site 3 out of 4 in 3rqd

Go back to Potassium Binding Sites List in 3rqd
Potassium binding site 3 out of 4 in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:17.9
occ:1.00
 O B:LEU200 2.7 11.6 1.0
O B:ASP178 2.8 21.5 1.0
O B:ASP176 3.0 16.2 1.0
O B:HIS180 3.0 15.3 1.0
OD1 B:ASP176 3.0 21.3 1.0
OG B:SER199 3.2 23.3 1.0
C B:ASP176 3.5 17.1 1.0
N B:ASP178 3.6 19.2 1.0
C B:ASP178 3.6 16.7 1.0
CG B:ASP176 3.7 23.2 1.0
C B:LEU200 3.7 22.0 1.0
CB B:HIS201 3.9 17.2 1.0
C B:HIS180 3.9 18.0 1.0
C B:LEU177 3.9 24.7 1.0
N B:LEU200 3.9 16.7 1.0
CB B:ASP176 4.0 15.8 1.0
CA B:ASP178 4.0 20.4 1.0
CB B:ASP178 4.0 16.0 1.0
N B:LEU177 4.1 22.1 1.0
CA B:LEU177 4.1 21.4 1.0
CB B:SER199 4.3 19.9 1.0
O B:HOH509 4.3 15.5 1.0
CA B:ASP176 4.4 19.7 1.0
CA B:HIS201 4.4 18.1 1.0
N B:GLY182 4.4 22.1 1.0
CA B:SER199 4.4 21.4 1.0
N B:HIS180 4.4 15.9 1.0
ND1 B:HIS201 4.4 18.1 1.0
N B:HIS201 4.4 22.4 1.0
C B:SER199 4.5 19.2 1.0
CA B:LEU200 4.5 20.3 1.0
CA B:HIS181 4.5 15.5 1.0
N B:HIS181 4.5 15.5 1.0
OD2 B:ASP176 4.5 28.2 1.0
C B:LEU179 4.6 21.3 1.0
O B:LEU177 4.6 16.2 1.0
CG B:HIS201 4.6 16.8 1.0
N B:LEU179 4.7 16.2 1.0
C B:HIS181 4.7 25.1 1.0
CA B:HIS180 4.8 12.6 1.0
O B:LEU179 4.8 15.2 1.0

Potassium binding site 4 out of 4 in 3rqd

Go back to Potassium Binding Sites List in 3rqd
Potassium binding site 4 out of 4 in the Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Ideal Thiolate-Zinc Coordination Geometry in Depsipeptide Binding to Histone Deacetylase 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:23.9
occ:1.00
 O B:VAL195 2.8 22.7 1.0
O B:HOH537 2.9 19.7 1.0
O B:PHE189 2.9 23.8 1.0
O B:THR192 3.0 17.5 1.0
O B:TYR225 3.1 20.4 1.0
O B:HOH527 3.2 20.5 1.0
CB B:TYR225 3.7 25.5 1.0
C B:PHE189 3.7 23.1 1.0
C B:TYR225 3.8 24.3 1.0
C B:VAL195 4.0 25.2 1.0
CB B:PHE189 4.0 22.4 1.0
OG B:SER226 4.1 20.3 1.0
C B:THR192 4.2 26.6 1.0
CA B:TYR225 4.4 20.1 1.0
CA B:SER190 4.4 23.2 1.0
CA B:MET196 4.4 20.8 1.0
N B:SER190 4.4 17.3 1.0
N B:THR197 4.5 21.9 1.0
N B:SER226 4.5 24.9 1.0
CA B:PHE189 4.6 26.7 1.0
CG2 B:THR192 4.6 15.8 1.0
O B:GLY222 4.6 21.7 1.0
C B:SER190 4.6 32.5 1.0
N B:MET196 4.7 23.6 1.0
N B:THR192 4.7 27.6 1.0
O B:SER190 4.7 27.2 1.0
OG1 B:THR197 4.7 26.0 1.0
C B:MET196 4.9 24.7 1.0
CG2 B:THR197 4.9 21.9 1.0
CA B:GLY222 4.9 24.7 1.0
CA B:SER226 4.9 19.4 1.0
CG B:TYR225 5.0 30.8 1.0

Reference:

K.E.Cole, D.P.Dowling, M.A.Boone, A.J.Phillips, D.W.Christianson. Structural Basis of the Antiproliferative Activity of Largazole, A Depsipeptide Inhibitor of the Histone Deacetylases. J.Am.Chem.Soc. V. 133 12474 2011.
ISSN: ISSN 0002-7863
PubMed: 21790156
DOI: 10.1021/JA205972N
Page generated: Mon Aug 12 09:21:20 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