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Potassium in PDB 2v5w: Crystal Structure of HDAC8-Substrate Complex

Protein crystallography data

The structure of Crystal Structure of HDAC8-Substrate Complex, PDB code: 2v5w was solved by S.Di Marco, A.Vannini, C.Volpari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.304, 151.801, 57.552, 90.00, 117.02, 90.00
R / Rfree (%) 17.6 / 23

Other elements in 2v5w:

The structure of Crystal Structure of HDAC8-Substrate 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-Substrate Complex (pdb code 2v5w). 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-Substrate Complex, PDB code: 2v5w:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 2v5w

Go back to Potassium Binding Sites List in 2v5w
Potassium binding site 1 out of 4 in the Crystal Structure of HDAC8-Substrate 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-Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1378

b:13.5
occ:1.00
 O A:LEU200 2.6 12.7 1.0
O A:ASP178 2.7 13.9 1.0
OD1 A:ASP176 2.8 12.6 1.0
O A:ASP176 2.8 13.4 1.0
O A:HIS180 2.8 13.0 1.0
OG A:SER199 2.9 16.0 1.0
C A:ASP176 3.5 13.1 1.0
CG A:ASP176 3.5 14.7 1.0
C A:LEU200 3.6 13.0 1.0
C A:ASP178 3.6 13.7 1.0
N A:ASP178 3.7 13.3 1.0
C A:HIS180 3.8 12.8 1.0
CB A:HIS201 3.8 13.8 1.0
N A:LEU200 3.9 12.9 1.0
CB A:ASP176 3.9 14.4 1.0
CA A:ASP178 4.0 13.5 1.0
CB A:ASP178 4.0 13.4 1.0
CB A:SER199 4.0 15.1 1.0
N A:LEU177 4.0 12.9 1.0
C A:LEU177 4.1 12.5 1.0
CA A:LEU177 4.2 13.3 1.0
ND1 A:HIS201 4.3 15.3 1.0
CA A:SER199 4.3 14.8 1.0
CA A:ASP176 4.3 14.4 1.0
OD2 A:ASP176 4.3 15.5 1.0
N A:GLY182 4.3 15.1 1.0
C A:SER199 4.4 14.3 1.0
CA A:HIS201 4.4 13.7 1.0
N A:HIS201 4.4 13.6 1.0
CA A:LEU200 4.4 13.9 1.0
CA A:HIS181 4.4 13.7 1.0
N A:HIS181 4.5 13.2 1.0
N A:HIS180 4.5 12.7 1.0
O A:HOH2236 4.5 9.6 1.0
CG A:HIS201 4.5 14.6 1.0
C A:LEU179 4.6 13.0 1.0
C A:HIS181 4.7 14.2 1.0
N A:LEU179 4.7 13.6 1.0
CA A:HIS180 4.8 12.1 1.0
CE1 A:HIS142 4.8 15.2 1.0
O A:LEU177 4.9 12.9 1.0
O A:LEU179 4.9 12.9 1.0

Potassium binding site 2 out of 4 in 2v5w

Go back to Potassium Binding Sites List in 2v5w
Potassium binding site 2 out of 4 in the Crystal Structure of HDAC8-Substrate 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-Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1379

b:15.4
occ:1.00
 O A:HOH2215 2.6 11.6 1.0
O A:VAL195 2.6 18.4 1.0
O A:HOH2220 2.7 14.3 1.0
O A:PHE189 2.7 19.6 1.0
O A:THR192 2.9 20.1 1.0
O A:TYR225 3.0 17.8 1.0
CB A:TYR225 3.5 18.2 1.0
C A:TYR225 3.6 17.7 1.0
C A:PHE189 3.7 19.6 1.0
C A:VAL195 3.8 18.8 1.0
OG A:SER226 4.0 15.7 1.0
C A:THR192 4.1 20.6 1.0
CA A:TYR225 4.2 18.2 1.0
CB A:PHE189 4.2 19.3 1.0
CA A:SER190 4.3 20.6 1.0
O A:SER190 4.3 20.5 1.0
N A:SER226 4.4 17.1 1.0
C A:SER190 4.4 20.6 1.0
N A:SER190 4.4 19.6 1.0
CA A:MET196 4.4 19.4 1.0
O A:GLY222 4.5 20.3 1.0
CA A:PHE189 4.6 19.2 1.0
N A:THR192 4.6 21.0 1.0
N A:THR197 4.6 18.9 1.0
N A:MET196 4.6 18.9 1.0
CG2 A:THR192 4.6 22.3 1.0
CG A:TYR225 4.8 18.9 1.0
CA A:VAL195 4.9 19.0 1.0
CA A:THR192 4.9 21.2 1.0
OG1 A:THR197 4.9 19.8 1.0
CA A:GLY222 4.9 22.8 1.0
CA A:SER226 5.0 16.4 1.0
CB A:VAL195 5.0 18.5 1.0
C A:MET196 5.0 18.8 1.0

Potassium binding site 3 out of 4 in 2v5w

Go back to Potassium Binding Sites List in 2v5w
Potassium binding site 3 out of 4 in the Crystal Structure of HDAC8-Substrate 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-Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1377

b:13.5
occ:1.00
 OD1 B:ASP176 2.7 12.6 1.0
O B:LEU200 2.7 12.7 1.0
O B:ASP178 2.8 12.5 1.0
O B:HIS180 2.8 15.4 1.0
O B:ASP176 2.8 13.6 1.0
OG B:SER199 3.0 13.2 1.0
CG B:ASP176 3.4 14.9 1.0
C B:ASP176 3.4 14.2 1.0
N B:ASP178 3.6 13.0 1.0
C B:ASP178 3.6 12.3 1.0
C B:LEU200 3.7 12.6 1.0
C B:HIS180 3.8 13.7 1.0
CB B:HIS201 3.8 11.9 1.0
CB B:ASP176 3.9 14.9 1.0
CA B:ASP178 3.9 13.3 1.0
CB B:ASP178 3.9 13.4 1.0
N B:LEU200 3.9 12.9 1.0
C B:LEU177 4.0 12.3 1.0
N B:LEU177 4.0 13.1 1.0
CB B:SER199 4.1 13.3 1.0
OD2 B:ASP176 4.2 15.7 1.0
CA B:LEU177 4.2 12.6 1.0
ND1 B:HIS201 4.2 12.8 1.0
CA B:ASP176 4.3 14.5 1.0
CA B:SER199 4.3 13.2 1.0
N B:GLY182 4.3 13.6 1.0
CA B:HIS201 4.4 12.1 1.0
CA B:HIS181 4.4 13.7 1.0
C B:SER199 4.4 13.2 1.0
O B:HOH2240 4.4 9.3 1.0
N B:HIS201 4.4 12.9 1.0
N B:HIS181 4.5 13.5 1.0
N B:HIS180 4.5 12.5 1.0
CA B:LEU200 4.5 13.4 1.0
CG B:HIS201 4.5 12.1 1.0
C B:LEU179 4.6 12.8 1.0
C B:HIS181 4.7 13.5 1.0
CA B:HIS180 4.7 12.8 1.0
N B:LEU179 4.7 12.9 1.0
O B:LEU177 4.8 12.0 1.0
CE1 B:HIS142 4.8 18.6 1.0
O B:LEU179 4.9 13.5 1.0

Potassium binding site 4 out of 4 in 2v5w

Go back to Potassium Binding Sites List in 2v5w
Potassium binding site 4 out of 4 in the Crystal Structure of HDAC8-Substrate 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-Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1378

b:16.9
occ:1.00
 O B:PHE189 2.6 19.4 1.0
O B:VAL195 2.6 16.6 1.0
O B:HOH2225 2.7 17.1 1.0
O B:HOH2220 2.7 17.7 1.0
O B:THR192 2.9 19.5 1.0
O B:TYR225 2.9 17.9 1.0
C B:PHE189 3.5 18.8 1.0
C B:TYR225 3.6 17.7 1.0
CB B:TYR225 3.6 18.1 1.0
C B:VAL195 3.8 17.3 1.0
OG B:SER226 4.0 15.5 1.0
CB B:PHE189 4.0 18.4 1.0
C B:THR192 4.1 20.7 1.0
CA B:TYR225 4.2 18.5 1.0
N B:SER190 4.3 19.3 1.0
CA B:SER190 4.4 20.2 1.0
O B:SER190 4.4 19.9 1.0
CA B:PHE189 4.4 19.0 1.0
CA B:MET196 4.4 17.1 1.0
C B:SER190 4.4 20.0 1.0
N B:SER226 4.5 16.5 1.0
N B:THR192 4.5 20.9 1.0
CG2 B:THR192 4.6 21.5 1.0
O B:GLY222 4.6 22.1 1.0
N B:MET196 4.6 17.2 1.0
N B:THR197 4.7 15.7 1.0
CA B:THR192 4.8 20.8 1.0
CA B:VAL195 4.9 17.7 1.0
CA B:GLY222 4.9 23.7 1.0
CA B:SER226 5.0 15.7 1.0
CG B:TYR225 5.0 20.0 1.0
C B:MET196 5.0 16.5 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 07:07:25 2024

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