Atomistry » Potassium » PDB 2qyo-2vxy » 2vqv
Atomistry »
  Potassium »
    PDB 2qyo-2vxy »
      2vqv »

Potassium in PDB 2vqv: Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor

Protein crystallography data

The structure of Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor, PDB code: 2vqv 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) 30.00 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.524, 70.766, 89.011, 90.00, 108.57, 90.00
R / Rfree (%) 23.4 / 26.5

Other elements in 2vqv:

The structure of Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor (pdb code 2vqv). 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 with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor, PDB code: 2vqv:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 2vqv

Go back to Potassium Binding Sites List in 2vqv
Potassium binding site 1 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor


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 with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1407

b:53.6
occ:1.00
O A:ASP194 2.6 30.9 1.0
O A:HIS198 2.6 32.4 1.0
O A:ASP196 2.8 31.7 1.0
OD1 A:ASP194 2.9 28.6 1.0
O A:LEU218 3.0 33.5 1.0
OG A:SER217 3.1 32.2 1.0
C A:ASP194 3.6 30.8 1.0
CG A:ASP194 3.7 30.1 1.0
C A:HIS198 3.7 32.5 1.0
C A:LEU218 3.8 33.4 1.0
C A:ASP196 3.8 31.7 1.0
CB A:HIS219 3.9 34.2 1.0
N A:ASP196 4.0 31.4 1.0
CB A:SER217 4.0 32.4 1.0
N A:LEU218 4.1 32.8 1.0
CB A:ASP194 4.1 30.5 1.0
CA A:SER217 4.3 32.4 1.0
CA A:HIS199 4.3 33.0 1.0
CA A:ASP196 4.3 31.6 1.0
C A:SER217 4.3 32.6 1.0
C A:TRP195 4.4 31.2 1.0
N A:TRP195 4.4 30.9 1.0
N A:HIS219 4.4 33.8 1.0
CB A:ASP196 4.4 31.7 1.0
N A:GLY200 4.4 33.1 1.0
CA A:HIS219 4.4 34.2 1.0
ND1 A:HIS219 4.4 34.8 1.0
CA A:TRP195 4.4 31.0 1.0
N A:HIS199 4.4 32.8 1.0
CA A:ASP194 4.5 30.5 1.0
N A:HIS198 4.5 32.2 1.0
O A:HOH2002 4.5 34.4 1.0
C A:VAL197 4.6 32.1 1.0
CA A:LEU218 4.6 33.1 1.0
CG A:HIS219 4.6 34.5 1.0
C A:HIS199 4.7 33.0 1.0
OD2 A:ASP194 4.7 30.0 1.0
CE1 A:HIS158 4.7 35.4 1.0
O A:VAL197 4.7 32.2 1.0
CA A:HIS198 4.7 32.3 1.0
N A:VAL197 4.9 31.8 1.0
OH A:TYR215 4.9 29.7 1.0
ND1 A:HIS158 5.0 34.9 1.0

Potassium binding site 2 out of 4 in 2vqv

Go back to Potassium Binding Sites List in 2vqv
Potassium binding site 2 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor


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 with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1408

b:69.2
occ:1.00
O A:PHE207 2.7 34.9 1.0
O A:PHE244 3.2 35.7 1.0
O A:ASP210 3.5 36.6 1.0
O A:VAL213 3.6 35.8 1.0
C A:PHE244 3.7 35.6 1.0
C A:PHE207 3.8 34.9 1.0
CB A:PHE244 4.0 36.5 1.0
O A:GLY241 4.0 39.7 1.0
N A:ASN245 4.1 34.7 1.0
CB A:ASN245 4.2 33.8 1.0
CA A:TYR208 4.3 36.0 1.0
C A:ASP210 4.3 36.5 1.0
CB A:PHE207 4.4 34.3 1.0
CA A:PHE244 4.4 36.4 1.0
C A:TYR208 4.4 36.3 1.0
CA A:ASN245 4.5 33.9 1.0
N A:TYR208 4.5 35.5 1.0
N A:ASP210 4.6 36.4 1.0
C A:VAL213 4.7 35.6 1.0
ND2 A:ASN245 4.7 32.9 1.0
O A:TYR208 4.7 36.6 1.0
CA A:PHE207 4.7 34.5 1.0
N A:SER209 4.8 36.4 1.0
N A:TYR215 4.9 33.2 1.0
CA A:GLY241 4.9 39.8 1.0
C A:GLY241 4.9 39.5 1.0

Potassium binding site 3 out of 4 in 2vqv

Go back to Potassium Binding Sites List in 2vqv
Potassium binding site 3 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor


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 with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1409

b:40.4
occ:1.00
O B:HIS198 2.5 32.5 1.0
O B:ASP194 2.6 30.9 1.0
O B:ASP196 2.9 31.6 1.0
OD1 B:ASP194 2.9 28.5 1.0
OG B:SER217 3.0 32.1 1.0
O B:LEU218 3.2 33.3 1.0
C B:HIS198 3.6 32.5 1.0
C B:ASP194 3.7 30.7 1.0
CG B:ASP194 3.7 30.0 1.0
C B:ASP196 3.8 31.6 1.0
C B:LEU218 3.9 33.4 1.0
CB B:HIS219 3.9 34.3 1.0
CB B:SER217 4.0 32.3 1.0
N B:ASP196 4.0 31.4 1.0
CB B:ASP194 4.1 30.5 1.0
N B:LEU218 4.1 32.8 1.0
CA B:HIS199 4.2 33.0 1.0
N B:GLY200 4.3 33.1 1.0
CA B:SER217 4.3 32.3 1.0
N B:HIS199 4.3 32.8 1.0
CA B:ASP196 4.3 31.7 1.0
C B:SER217 4.4 32.5 1.0
ND1 B:HIS219 4.4 34.8 1.0
CB B:ASP196 4.4 31.8 1.0
CA B:HIS219 4.4 34.2 1.0
N B:HIS219 4.4 33.8 1.0
C B:TRP195 4.5 31.2 1.0
N B:HIS198 4.5 32.2 1.0
N B:TRP195 4.5 30.9 1.0
CA B:ASP194 4.5 30.5 1.0
C B:HIS199 4.5 32.9 1.0
CA B:TRP195 4.6 30.9 1.0
C B:VAL197 4.6 32.1 1.0
CG B:HIS219 4.6 34.5 1.0
CE1 B:HIS158 4.6 35.6 1.0
OD2 B:ASP194 4.7 29.9 1.0
CA B:LEU218 4.7 33.1 1.0
CA B:HIS198 4.7 32.2 1.0
O B:VAL197 4.7 32.2 1.0
OH B:TYR215 4.9 29.7 1.0
N B:VAL197 4.9 31.7 1.0
ND1 B:HIS158 4.9 35.0 1.0

Potassium binding site 4 out of 4 in 2vqv

Go back to Potassium Binding Sites List in 2vqv
Potassium binding site 4 out of 4 in the Structure of HDAC4 Catalytic Domain with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor


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 with A Gain-of-Function Mutation Bound to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1410

b:64.4
occ:1.00
O B:PHE207 2.6 34.9 1.0
O B:PHE244 3.4 35.5 1.0
O B:ASP210 3.4 36.7 1.0
O B:VAL213 3.6 35.8 1.0
C B:PHE207 3.7 34.9 1.0
C B:PHE244 3.8 35.6 1.0
O B:GLY241 4.0 39.5 1.0
CB B:PHE244 4.0 36.6 1.0
C B:ASP210 4.2 36.5 1.0
N B:ASN245 4.2 34.7 1.0
CA B:TYR208 4.3 36.0 1.0
CB B:PHE207 4.3 34.3 1.0
CB B:ASN245 4.3 33.8 1.0
C B:TYR208 4.4 36.2 1.0
N B:ASP210 4.4 36.4 1.0
N B:TYR208 4.5 35.5 1.0
CA B:PHE244 4.5 36.4 1.0
CA B:ASN245 4.6 33.8 1.0
CA B:PHE207 4.7 34.5 1.0
C B:VAL213 4.7 35.5 1.0
N B:SER209 4.7 36.4 1.0
O B:TYR208 4.8 36.5 1.0
CA B:GLY241 4.8 39.7 1.0
C B:GLY241 4.8 39.5 1.0
ND2 B:ASN245 4.9 32.9 1.0
CA B:ASP210 4.9 36.3 1.0
N B:PRO211 5.0 36.7 1.0
N B:TYR215 5.0 33.2 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 Structural Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200
Page generated: Sun Dec 13 23:12:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy