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Potassium in PDB 1w22: Crystal Structure of Inhibited Human HDAC8

Protein crystallography data

The structure of Crystal Structure of Inhibited Human HDAC8, PDB code: 1w22 was solved by A.Vannini, C.Volpari, E.Caroli Casavola, S.Di Marco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.0 / 2.5
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.746, 83.532, 94.653, 90.00, 97.48, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1w22:

The structure of Crystal Structure of Inhibited Human HDAC8 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Inhibited Human HDAC8 (pdb code 1w22). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Inhibited Human HDAC8, PDB code: 1w22:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 1w22

Go back to Potassium Binding Sites List in 1w22
Potassium binding site 1 out of 4 in the Crystal Structure of Inhibited Human HDAC8


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 Inhibited Human HDAC8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1376

b:21.6
occ:1.00
 O A:HIS180 2.8 23.8 1.0
O A:LEU200 2.9 22.9 1.0
O A:ASP178 2.9 22.9 1.0
OD1 A:ASP176 3.0 25.8 1.0
O A:ASP176 3.1 24.7 1.0
OG A:SER199 3.1 24.9 1.0
N A:ASP178 3.4 20.0 1.0
CG A:ASP176 3.5 26.6 1.0
C A:ASP176 3.6 24.9 1.0
C A:LEU200 3.7 25.7 1.0
C A:ASP178 3.7 20.3 1.0
CB A:ASP176 3.8 25.6 1.0
N A:LEU200 3.8 26.7 1.0
C A:HIS180 3.9 21.0 1.0
CB A:HIS201 3.9 22.4 1.0
CA A:ASP178 4.0 19.7 1.0
C A:LEU177 4.0 23.0 1.0
CB A:ASP178 4.0 19.7 1.0
N A:LEU177 4.1 24.2 1.0
CA A:LEU177 4.2 23.5 1.0
CB A:SER199 4.2 24.5 1.0
ND1 A:HIS201 4.3 22.4 1.0
CA A:ASP176 4.3 26.0 1.0
OD2 A:ASP176 4.3 25.8 1.0
N A:GLY182 4.4 22.3 1.0
C A:SER199 4.4 27.1 1.0
N A:HIS201 4.4 26.0 1.0
CA A:HIS201 4.4 25.8 1.0
CA A:HIS181 4.4 19.4 1.0
CA A:SER199 4.4 26.4 1.0
O A:HOH2103 4.4 13.2 1.0
CA A:LEU200 4.4 24.9 1.0
CG A:HIS201 4.5 23.8 1.0
N A:HIS181 4.6 20.1 1.0
N A:HIS180 4.6 19.3 1.0
C A:LEU179 4.7 20.7 1.0
C A:HIS181 4.7 20.5 1.0
N A:LEU179 4.7 21.8 1.0
O A:LEU177 4.8 25.7 1.0
CA A:HIS180 4.8 19.7 1.0
O A:LEU179 4.8 21.3 1.0
CE1 A:HIS142 4.9 25.3 1.0

Potassium binding site 2 out of 4 in 1w22

Go back to Potassium Binding Sites List in 1w22
Potassium binding site 2 out of 4 in the Crystal Structure of Inhibited Human HDAC8


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 Inhibited Human HDAC8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1377

b:42.7
occ:1.00
 O A:VAL195 2.8 25.7 1.0
O A:PHE189 2.9 24.5 1.0
O A:HOH2093 3.1 41.1 1.0
O A:HOH2074 3.1 38.8 1.0
O A:THR192 3.1 33.2 1.0
O A:TYR225 3.1 30.6 1.0
CB A:TYR225 3.6 35.1 1.0
C A:PHE189 3.7 26.8 1.0
C A:TYR225 3.8 33.2 1.0
C A:VAL195 3.9 27.2 1.0
CB A:PHE189 3.9 25.9 1.0
OG A:SER226 4.0 36.0 1.0
C A:THR192 4.3 31.7 1.0
CA A:TYR225 4.3 34.8 1.0
CA A:MET196 4.3 28.4 1.0
CA A:SER190 4.3 32.2 1.0
N A:SER190 4.4 28.9 1.0
CA A:PHE189 4.5 28.1 1.0
N A:THR197 4.5 27.4 1.0
O A:GLY222 4.5 46.4 1.0
N A:MET196 4.6 26.6 1.0
C A:SER190 4.6 32.2 1.0
N A:SER226 4.6 33.4 1.0
O A:SER190 4.7 29.9 1.0
CG2 A:THR192 4.7 27.2 1.0
CG A:TYR225 4.8 35.5 1.0
N A:THR192 4.8 33.4 1.0
CA A:GLY222 4.9 46.9 1.0
OG1 A:THR197 4.9 31.1 1.0
CA A:VAL195 4.9 26.8 1.0
C A:MET196 4.9 28.3 1.0
CG2 A:THR197 5.0 29.4 1.0
CA A:SER226 5.0 35.8 1.0

Potassium binding site 3 out of 4 in 1w22

Go back to Potassium Binding Sites List in 1w22
Potassium binding site 3 out of 4 in the Crystal Structure of Inhibited Human HDAC8


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Inhibited Human HDAC8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1376

b:31.1
occ:1.00
 O B:ASP178 2.8 22.6 1.0
O B:ASP176 2.9 24.8 1.0
O B:HIS180 2.9 22.9 1.0
O B:LEU200 3.0 31.4 1.0
OG B:SER199 3.0 23.4 1.0
OD1 B:ASP176 3.0 23.8 1.0
N B:ASP178 3.4 22.5 1.0
C B:ASP176 3.5 25.3 1.0
CG B:ASP176 3.5 24.7 1.0
C B:ASP178 3.6 22.7 1.0
CB B:HIS201 3.6 27.9 1.0
C B:LEU200 3.7 29.8 1.0
C B:HIS180 3.7 22.9 1.0
CB B:ASP176 3.8 25.3 1.0
CA B:ASP178 3.9 22.2 1.0
N B:LEU200 3.9 28.9 1.0
C B:LEU177 3.9 22.3 1.0
CB B:ASP178 4.0 20.2 1.0
N B:LEU177 4.1 23.4 1.0
CA B:LEU177 4.2 23.2 1.0
CB B:SER199 4.2 25.4 1.0
CD2 B:HIS201 4.3 29.8 1.0
CA B:HIS201 4.3 31.2 1.0
CA B:ASP176 4.3 27.1 1.0
OD2 B:ASP176 4.3 24.8 1.0
CG B:HIS201 4.3 29.9 1.0
N B:HIS201 4.3 30.8 1.0
CA B:HIS181 4.4 26.1 1.0
N B:HIS181 4.4 23.6 1.0
N B:GLY182 4.4 26.4 1.0
C B:SER199 4.4 28.6 1.0
CA B:SER199 4.5 27.7 1.0
N B:HIS180 4.5 21.2 1.0
CA B:LEU200 4.5 29.8 1.0
O B:HOH2066 4.6 20.8 1.0
CA B:HIS180 4.7 20.3 1.0
C B:LEU179 4.7 20.6 1.0
C B:HIS181 4.7 25.8 1.0
O B:LEU177 4.7 24.8 1.0
N B:LEU179 4.7 22.3 1.0
CE1 B:HIS142 4.9 24.3 1.0

Potassium binding site 4 out of 4 in 1w22

Go back to Potassium Binding Sites List in 1w22
Potassium binding site 4 out of 4 in the Crystal Structure of Inhibited Human HDAC8


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Inhibited Human HDAC8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1377

b:40.5
occ:1.00
 O B:PHE189 2.8 34.2 1.0
O B:VAL195 2.9 39.6 1.0
O B:HOH2060 3.1 28.0 1.0
O B:THR192 3.2 42.4 1.0
O B:TYR225 3.2 43.4 1.0
O B:HOH2063 3.2 47.1 1.0
CB B:TYR225 3.5 43.9 1.0
C B:PHE189 3.6 36.8 1.0
C B:TYR225 3.7 43.2 1.0
OG B:SER226 3.9 43.3 1.0
C B:VAL195 4.1 40.0 1.0
CB B:PHE189 4.2 32.1 1.0
CA B:TYR225 4.2 44.8 1.0
CA B:SER190 4.2 41.7 1.0
N B:SER190 4.3 39.5 1.0
O B:SER190 4.3 44.1 1.0
C B:THR192 4.4 42.4 1.0
N B:SER226 4.4 41.7 1.0
CA B:MET196 4.4 38.3 1.0
C B:SER190 4.4 43.0 1.0
O B:GLY222 4.5 46.0 1.0
N B:THR197 4.5 36.0 1.0
CA B:PHE189 4.6 35.1 1.0
OG1 B:THR197 4.6 32.5 1.0
CG2 B:THR192 4.7 36.9 1.0
N B:MET196 4.7 39.1 1.0
N B:THR192 4.7 41.3 1.0
CG B:TYR225 4.8 44.9 1.0
CA B:SER226 4.8 41.2 1.0
CA B:GLY222 4.8 48.0 1.0
CB B:SER226 4.9 39.7 1.0
CG2 B:THR197 4.9 32.7 1.0
C B:MET196 4.9 36.5 1.0

Reference:

A.Vannini, C.Volpari, G.Filocamo, E.Caroli Casavola, M.Brunetti, D.Renzoni, P.Chakravarty, C.Paolini, R.De Francesco, P.Gallinari, C.Steinckuhler, S.Di Marco. Crystal Structure of A Eukaryotic Zn-Dependent Histone Deacetylase,Human HDAC8,Complexed with A Hydroxamic Acid Inhibitor Proc.Natl.Acad.Sci.Usa V. 101 15064 2004.
ISSN: ISSN 0027-8424
PubMed: 15477595
DOI: 10.1073/PNAS.0404603101
Page generated: Mon Aug 12 05:40:06 2024

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