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Potassium in PDB 2v5x: Crystal Structure of HDAC8-Inhibitor Complex

Protein crystallography data

The structure of Crystal Structure of HDAC8-Inhibitor Complex, PDB code: 2v5x was solved by S.Di Marco, A.Vannini, C.Volpari, P.Gallinari, P.Jones, M.Mattu, A.Carfi, R.Defrancesco, C.Steinkuhler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.298, 98.694, 110.474, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24

Other elements in 2v5x:

The structure of Crystal Structure of HDAC8-Inhibitor Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of HDAC8-Inhibitor Complex (pdb code 2v5x). 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 HDAC8-Inhibitor Complex, PDB code: 2v5x:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 2v5x

Go back to Potassium Binding Sites List in 2v5x
Potassium binding site 1 out of 4 in the Crystal Structure of HDAC8-Inhibitor Complex


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 HDAC8-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1378

b:24.7
occ:1.00
 O A:ASP178 2.7 23.8 1.0
O A:LEU200 2.7 25.4 1.0
OD1 A:ASP176 2.7 26.7 1.0
O A:HIS180 2.8 25.4 1.0
OG A:SER199 2.8 24.0 1.0
O A:ASP176 2.8 23.4 1.0
C A:ASP176 3.5 24.4 1.0
CG A:ASP176 3.5 25.1 1.0
C A:ASP178 3.5 24.2 1.0
C A:LEU200 3.6 25.8 1.0
N A:ASP178 3.6 24.5 1.0
C A:HIS180 3.7 25.8 1.0
CB A:HIS201 3.8 26.8 1.0
CA A:ASP178 3.9 24.1 1.0
CB A:ASP176 3.9 25.9 1.0
CB A:ASP178 3.9 24.4 1.0
N A:LEU200 4.0 25.4 1.0
N A:LEU177 4.0 24.6 1.0
CB A:SER199 4.1 25.1 1.0
C A:LEU177 4.1 25.0 1.0
CA A:LEU177 4.2 24.5 1.0
N A:GLY182 4.3 27.8 1.0
CA A:ASP176 4.3 25.2 1.0
N A:HIS181 4.3 26.6 1.0
ND1 A:HIS201 4.3 30.0 1.0
OD2 A:ASP176 4.3 24.9 1.0
CA A:HIS201 4.3 26.6 1.0
CA A:HIS181 4.4 27.7 1.0
N A:HIS201 4.4 25.8 1.0
CG A:HIS201 4.4 28.1 1.0
N A:HIS180 4.4 25.3 1.0
CA A:SER199 4.5 25.3 1.0
CA A:LEU200 4.5 25.4 1.0
C A:SER199 4.6 25.6 1.0
C A:HIS181 4.6 28.0 1.0
O A:HOH2070 4.6 24.5 1.0
C A:LEU179 4.6 24.9 1.0
N A:LEU179 4.6 24.3 1.0
CA A:HIS180 4.7 25.2 1.0
CE1 A:HIS142 4.8 25.9 1.0
O A:LEU177 4.9 26.0 1.0
O A:LEU179 5.0 24.2 1.0

Potassium binding site 2 out of 4 in 2v5x

Go back to Potassium Binding Sites List in 2v5x
Potassium binding site 2 out of 4 in the Crystal Structure of HDAC8-Inhibitor Complex


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 HDAC8-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1379

b:28.4
occ:1.00
 O A:VAL195 2.6 29.9 1.0
O A:PHE189 2.6 31.3 1.0
O A:HOH2086 2.7 25.5 1.0
O A:HOH2064 2.8 23.6 1.0
O A:TYR225 2.9 35.9 1.0
O A:THR192 2.9 32.8 1.0
C A:PHE189 3.6 32.8 1.0
C A:TYR225 3.8 35.4 1.0
C A:VAL195 3.8 30.1 1.0
CB A:TYR225 3.8 36.7 1.0
OG A:SER226 3.9 32.9 1.0
CB A:PHE189 4.0 32.5 1.0
C A:THR192 4.1 33.3 1.0
CA A:SER190 4.3 35.2 1.0
N A:SER190 4.4 33.8 1.0
CA A:PHE189 4.4 32.5 1.0
CA A:MET196 4.4 29.9 1.0
CA A:TYR225 4.4 36.4 1.0
O A:SER190 4.5 35.1 1.0
C A:SER190 4.5 35.2 1.0
N A:MET196 4.5 29.6 1.0
N A:SER226 4.6 34.2 1.0
CG2 A:THR192 4.6 33.4 1.0
N A:THR197 4.7 28.0 1.0
O A:GLY222 4.7 41.0 1.0
N A:THR192 4.7 34.5 1.0
CA A:VAL195 4.8 30.3 1.0
CG2 A:THR197 4.9 24.5 1.0
CB A:VAL195 4.9 30.1 1.0
CA A:THR192 4.9 33.6 1.0
OG1 A:THR197 4.9 27.4 1.0

Potassium binding site 3 out of 4 in 2v5x

Go back to Potassium Binding Sites List in 2v5x
Potassium binding site 3 out of 4 in the Crystal Structure of HDAC8-Inhibitor Complex


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 HDAC8-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1378

b:25.8
occ:1.00
 O B:ASP178 2.6 27.0 1.0
O B:ASP176 2.6 28.7 1.0
O B:LEU200 2.7 26.3 1.0
O B:HIS180 2.7 25.8 1.0
OD1 B:ASP176 2.8 25.4 1.0
OG B:SER199 2.9 27.1 1.0
C B:ASP176 3.4 28.2 1.0
CG B:ASP176 3.5 26.8 1.0
C B:ASP178 3.5 27.0 1.0
C B:LEU200 3.5 27.4 1.0
N B:ASP178 3.6 26.9 1.0
C B:HIS180 3.8 26.4 1.0
CB B:HIS201 3.9 27.6 1.0
N B:LEU200 3.9 27.6 1.0
CA B:ASP178 3.9 27.2 1.0
CB B:ASP178 4.0 27.1 1.0
CB B:ASP176 4.0 27.7 1.0
C B:LEU177 4.0 27.1 1.0
N B:LEU177 4.0 27.5 1.0
CB B:SER199 4.2 27.6 1.0
CA B:LEU177 4.2 27.0 1.0
OD2 B:ASP176 4.3 26.7 1.0
CA B:ASP176 4.3 27.9 1.0
N B:HIS201 4.3 27.8 1.0
ND1 B:HIS201 4.3 31.0 1.0
CA B:HIS201 4.3 27.9 1.0
CA B:SER199 4.4 27.7 1.0
CA B:LEU200 4.4 27.7 1.0
N B:GLY182 4.4 29.1 1.0
O B:HOH2097 4.4 23.3 1.0
N B:HIS180 4.5 26.6 1.0
C B:SER199 4.5 28.1 1.0
CA B:HIS181 4.5 28.3 1.0
N B:HIS181 4.5 27.0 1.0
CG B:HIS201 4.6 28.8 1.0
C B:LEU179 4.6 27.2 1.0
N B:LEU179 4.6 27.1 1.0
CA B:HIS180 4.8 25.9 1.0
O B:LEU177 4.8 26.8 1.0
CE1 B:HIS142 4.8 28.0 1.0
C B:HIS181 4.8 28.6 1.0
O B:LEU179 4.9 27.5 1.0

Potassium binding site 4 out of 4 in 2v5x

Go back to Potassium Binding Sites List in 2v5x
Potassium binding site 4 out of 4 in the Crystal Structure of HDAC8-Inhibitor Complex


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 HDAC8-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1379

b:32.6
occ:1.00
 O B:PHE189 2.5 31.6 1.0
O B:HOH2092 2.6 29.9 1.0
O B:VAL195 2.6 29.8 1.0
O B:HOH2069 2.7 32.2 1.0
O B:THR192 2.8 32.5 1.0
O B:TYR225 3.1 39.9 1.0
C B:PHE189 3.6 32.2 1.0
CB B:TYR225 3.8 40.4 1.0
C B:TYR225 3.8 40.1 1.0
C B:VAL195 3.9 30.6 1.0
C B:THR192 4.0 32.6 1.0
CB B:PHE189 4.1 31.8 1.0
OG B:SER226 4.1 39.1 1.0
CA B:TYR225 4.4 40.3 1.0
CA B:MET196 4.4 30.9 1.0
O B:SER190 4.4 32.6 1.0
CA B:SER190 4.4 33.3 1.0
N B:SER190 4.4 32.3 1.0
CA B:PHE189 4.5 32.5 1.0
CG2 B:THR192 4.5 33.9 1.0
N B:SER226 4.5 39.6 1.0
C B:SER190 4.5 33.1 1.0
O B:GLY222 4.6 42.0 1.0
N B:MET196 4.6 31.0 1.0
N B:THR197 4.6 29.6 1.0
N B:THR192 4.6 32.8 1.0
CA B:THR192 4.8 32.6 1.0
CA B:VAL195 4.9 31.2 1.0
CA B:GLY222 4.9 42.9 1.0
N B:SER193 4.9 32.3 1.0
C B:MET196 5.0 30.4 1.0
OG1 B:THR197 5.0 28.1 1.0

Reference:

A.Vannini, C.Volpari, P.Gallinari, P.Jones, M.Mattu, A.Carfi, R.Defrancesco, C.Steinkuhler, S.Di Marco. Substrate Binding to Histone Deacetylases As Revealed By Crystal Structure of HDAC8-Substrate Complex Embo Rep. V. 8 879 2007.
ISSN: ISSN 1469-221X
PubMed: 17721440
DOI: 10.1038/SJ.EMBOR.7401047
Page generated: Mon Aug 12 07:08:18 2024

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