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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

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