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Potassium in PDB 2vqq: Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor

Protein crystallography data

The structure of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqq was solved by M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 1.9
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.605, 70.673, 88.201, 90.00, 108.08, 90.00
R / Rfree (%) 19.4 / 22.1

Other elements in 2vqq:

The structure of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor (pdb code 2vqq). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqq:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 2vqq

Go back to Potassium Binding Sites List in 2vqq
Potassium binding site 1 out of 4 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1408

b:31.4
occ:1.00
 O A:ASP196 2.7 11.5 1.0
OG A:SER217 2.8 14.5 1.0
O A:LEU218 2.8 13.3 1.0
O A:ASP194 2.9 11.3 1.0
O A:HIS198 2.9 12.6 1.0
OD1 A:ASP194 2.9 12.2 1.0
CG A:ASP194 3.4 13.2 1.0
C A:ASP194 3.6 11.7 1.0
C A:HIS198 3.8 11.9 1.0
C A:ASP196 3.8 11.4 1.0
C A:LEU218 3.8 13.7 1.0
CB A:HIS219 3.9 13.8 1.0
CB A:ASP194 3.9 12.4 1.0
N A:ASP196 4.0 11.8 1.0
CB A:SER217 4.0 15.3 1.0
OD2 A:ASP194 4.0 13.6 1.0
N A:LEU218 4.1 13.8 1.0
CA A:HIS199 4.1 12.4 1.0
N A:GLY200 4.2 12.7 1.0
N A:TRP195 4.2 11.6 1.0
N A:HIS199 4.3 12.3 1.0
CA A:ASP196 4.3 11.6 1.0
C A:TRP195 4.3 11.8 1.0
CA A:SER217 4.3 14.9 1.0
CA A:ASP194 4.3 12.3 1.0
CB A:ASP196 4.4 11.6 1.0
CA A:TRP195 4.4 11.7 1.0
ND1 A:HIS219 4.5 13.8 1.0
CA A:HIS219 4.5 14.1 1.0
C A:HIS199 4.5 12.5 1.0
C A:SER217 4.5 14.7 1.0
N A:HIS219 4.5 13.3 1.0
N A:HIS198 4.5 11.4 1.0
CG A:HIS219 4.6 14.2 1.0
CA A:LEU218 4.6 13.9 1.0
OH A:TYR215 4.8 15.6 1.0
CA A:HIS198 4.8 11.8 1.0
CE1 A:HIS158 4.8 13.4 1.0
C A:VAL197 4.8 11.7 1.0
N A:VAL197 4.9 11.7 1.0
O A:HOH2171 4.9 14.8 1.0
ND1 A:HIS158 4.9 13.4 1.0

Potassium binding site 2 out of 4 in 2vqq

Go back to Potassium Binding Sites List in 2vqq
Potassium binding site 2 out of 4 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1409

b:39.9
occ:1.00
 O A:PHE207 2.7 19.8 1.0
O A:HOH2154 2.7 19.9 1.0
O A:VAL213 2.7 20.1 1.0
O A:ASP210 3.0 23.4 1.0
O A:HOH2156 3.0 20.0 1.0
O A:PHE244 3.1 20.6 1.0
C A:PHE207 3.7 19.5 1.0
C A:PHE244 3.8 20.8 1.0
CB A:PHE207 3.9 18.7 1.0
C A:VAL213 4.0 20.1 1.0
CB A:PHE244 4.0 21.4 1.0
C A:ASP210 4.1 23.4 1.0
CA A:PHE207 4.4 19.2 1.0
N A:TYR215 4.5 17.6 1.0
N A:ASN245 4.5 20.0 1.0
N A:TYR208 4.5 20.2 1.0
CA A:TYR208 4.5 21.0 1.0
CA A:PHE244 4.5 21.4 1.0
N A:ASP210 4.5 23.5 1.0
O A:TYR208 4.6 21.4 1.0
C A:TYR208 4.6 21.6 1.0
CA A:ASP210 4.7 23.3 1.0
CA A:ASN245 4.8 19.4 1.0
CB A:ASN245 4.8 19.0 1.0
CB A:TYR215 4.8 16.7 1.0
CA A:LEU214 4.8 19.2 1.0
N A:LEU214 4.8 19.6 1.0
CB A:ASP210 4.8 23.3 1.0
ND2 A:ASN245 4.9 16.9 1.0
CA A:VAL213 4.9 20.3 1.0
CB A:VAL213 4.9 20.6 1.0
O A:GLY241 4.9 26.5 1.0

Potassium binding site 3 out of 4 in 2vqq

Go back to Potassium Binding Sites List in 2vqq
Potassium binding site 3 out of 4 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1407

b:32.3
occ:1.00
 O B:ASP196 2.7 11.7 1.0
O B:HIS198 2.8 15.0 1.0
OG B:SER217 2.9 15.7 1.0
O B:ASP194 2.9 13.0 1.0
O B:LEU218 2.9 13.3 1.0
OD1 B:ASP194 2.9 13.1 1.0
CG B:ASP194 3.4 14.8 1.0
C B:ASP194 3.5 12.6 1.0
C B:HIS198 3.7 14.0 1.0
C B:ASP196 3.7 11.7 1.0
C B:LEU218 3.8 13.9 1.0
CB B:ASP194 3.9 13.0 1.0
CB B:HIS219 3.9 13.9 1.0
N B:ASP196 4.0 12.2 1.0
CB B:SER217 4.0 15.2 1.0
OD2 B:ASP194 4.0 16.1 1.0
N B:LEU218 4.1 13.8 1.0
CA B:HIS199 4.1 14.5 1.0
N B:TRP195 4.2 12.7 1.0
N B:HIS199 4.2 14.4 1.0
CA B:ASP196 4.2 11.8 1.0
N B:GLY200 4.3 14.1 1.0
CB B:ASP196 4.3 12.2 1.0
CA B:ASP194 4.3 13.1 1.0
C B:TRP195 4.3 12.3 1.0
CA B:TRP195 4.4 12.6 1.0
CA B:SER217 4.4 15.1 1.0
ND1 B:HIS219 4.5 14.9 1.0
C B:SER217 4.5 14.4 1.0
C B:HIS199 4.5 14.3 1.0
CA B:HIS219 4.5 14.4 1.0
N B:HIS219 4.5 13.9 1.0
N B:HIS198 4.6 12.8 1.0
CA B:LEU218 4.6 13.8 1.0
CG B:HIS219 4.6 14.7 1.0
CA B:HIS198 4.7 13.4 1.0
CE1 B:HIS158 4.7 13.7 1.0
C B:VAL197 4.8 12.6 1.0
N B:VAL197 4.8 11.9 1.0
OH B:TYR215 4.8 14.4 1.0
O B:HOH2228 4.9 13.4 1.0
ND1 B:HIS158 4.9 13.7 1.0

Potassium binding site 4 out of 4 in 2vqq

Go back to Potassium Binding Sites List in 2vqq
Potassium binding site 4 out of 4 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1408

b:36.4
occ:1.00
 O B:PHE207 2.6 20.6 1.0
O B:HOH2209 2.8 21.1 1.0
O B:VAL213 2.8 20.3 1.0
O B:HOH2212 2.9 16.2 1.0
O B:ASP210 3.1 21.8 1.0
O B:PHE244 3.1 21.4 1.0
C B:PHE207 3.6 20.1 1.0
C B:PHE244 3.8 21.6 1.0
CB B:PHE207 3.9 19.6 1.0
C B:VAL213 4.0 19.3 1.0
CB B:PHE244 4.1 22.4 1.0
C B:ASP210 4.2 21.9 1.0
CA B:PHE207 4.4 19.6 1.0
N B:TYR208 4.4 20.5 1.0
CA B:TYR208 4.4 21.0 1.0
N B:TYR215 4.5 16.8 1.0
N B:ASN245 4.5 20.8 1.0
N B:ASP210 4.5 21.9 1.0
CA B:PHE244 4.6 22.4 1.0
C B:TYR208 4.6 21.3 1.0
O B:TYR208 4.6 21.3 1.0
CB B:ASN245 4.7 19.9 1.0
ND2 B:ASN245 4.8 16.2 1.0
CB B:TYR215 4.8 16.2 1.0
CA B:ASN245 4.8 20.2 1.0
CA B:ASP210 4.8 21.8 1.0
CA B:LEU214 4.8 18.0 1.0
N B:LEU214 4.9 18.6 1.0
O B:GLY241 4.9 25.6 1.0
CA B:VAL213 4.9 19.8 1.0
CB B:VAL213 4.9 20.1 1.0
CB B:ASP210 4.9 21.7 1.0

Reference:

M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi. Structural and Functional Analysis of the Human HDAC4 Catalytic Domain Reveals A Regulatory Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200
Page generated: Mon Aug 12 07:16:35 2024

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