Atomistry » Potassium » PDB 6u9t-6v7h » 6uo2
Atomistry »
  Potassium »
    PDB 6u9t-6v7h »
      6uo2 »

Potassium in PDB 6uo2: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A, PDB code: 6uo2 was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.68 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.030, 124.261, 55.520, 90.00, 114.09, 90.00
R / Rfree (%) 18.7 / 22.2

Other elements in 6uo2:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A (pdb code 6uo2). 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A, PDB code: 6uo2:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6uo2

Go back to Potassium Binding Sites List in 6uo2
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:24.2
occ:1.00
 O A:VAL247 2.6 19.6 1.0
O A:PHE241 2.7 17.5 1.0
O A:HOH644 2.7 21.4 1.0
O A:ASP244 2.9 21.0 1.0
O A:TYR280 2.9 16.3 1.0
O A:HOH630 2.9 17.3 1.0
C A:PHE241 3.6 17.8 1.0
CB A:PHE241 3.7 18.2 1.0
C A:TYR280 3.7 18.6 1.0
CB A:TYR280 3.8 19.5 1.0
C A:VAL247 3.9 18.8 1.0
C A:ASP244 4.0 22.1 1.0
CA A:PHE241 4.3 18.1 1.0
N A:TYR249 4.4 16.9 1.0
CA A:TYR280 4.4 15.5 1.0
N A:ASN281 4.4 16.6 1.0
N A:ASP244 4.5 18.4 1.0
CA A:LEU248 4.5 15.9 1.0
N A:GLU242 4.6 17.8 1.0
O A:GLU242 4.6 20.3 1.0
CA A:ASP244 4.7 21.8 1.0
N A:LEU248 4.7 17.7 1.0
CB A:ASN281 4.7 17.0 1.0
CA A:GLU242 4.7 18.8 1.0
C A:GLU242 4.7 22.5 1.0
CB A:ASP244 4.7 18.1 1.0
CA A:ASN281 4.7 14.1 1.0
CA A:VAL247 4.9 19.4 1.0
C A:LEU248 4.9 15.4 1.0
CB A:TYR249 4.9 15.6 1.0
OD1 A:ASN281 4.9 15.8 1.0
CG A:PHE241 4.9 16.0 1.0
O A:GLY277 5.0 18.9 1.0

Potassium binding site 2 out of 4 in 6uo2

Go back to Potassium Binding Sites List in 6uo2
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:18.2
occ:1.00
 O A:ASP230 2.6 17.8 1.0
OG A:SER251 2.7 16.6 1.0
OD1 A:ASP228 2.8 15.7 1.0
O A:HIS232 2.8 17.3 1.0
O A:VAL252 2.9 15.8 1.0
O A:ASP228 2.9 14.8 1.0
CG A:ASP228 3.2 16.1 1.0
C A:ASP228 3.5 15.9 1.0
C A:ASP230 3.6 15.8 1.0
C A:HIS232 3.7 17.1 1.0
C A:VAL252 3.8 16.1 1.0
CB A:ASP228 3.8 14.0 1.0
N A:ASP230 3.8 13.9 1.0
CB A:HIS253 3.9 14.7 1.0
OD2 A:ASP228 3.9 16.6 1.0
N A:VAL252 3.9 17.2 1.0
CB A:SER251 3.9 15.0 1.0
CA A:ASP230 4.1 12.4 1.0
C A:TRP229 4.2 17.2 1.0
N A:TRP229 4.2 14.5 1.0
CA A:SER251 4.2 15.4 1.0
ND1 A:HIS253 4.3 16.0 1.0
CB A:ASP230 4.3 14.4 1.0
CA A:ASP228 4.3 13.5 1.0
CA A:HIS233 4.3 14.5 1.0
CA A:TRP229 4.3 14.2 1.0
C A:SER251 4.4 18.3 1.0
N A:HIS233 4.4 16.6 1.0
N A:HIS232 4.5 15.1 1.0
CA A:HIS253 4.5 14.8 1.0
CA A:VAL252 4.5 16.7 1.0
N A:GLY234 4.5 14.4 1.0
N A:HIS253 4.5 15.7 1.0
CG A:HIS253 4.5 15.3 1.0
C A:VAL231 4.7 18.2 1.0
N A:VAL231 4.7 15.2 1.0
CA A:HIS232 4.7 15.8 1.0
O A:HOH617 4.8 20.7 1.0
OH A:TYR249 4.8 14.8 1.0
C A:HIS233 4.9 17.6 1.0
O A:TRP229 4.9 15.8 1.0
CE1 A:HIS192 4.9 15.1 1.0

Potassium binding site 3 out of 4 in 6uo2

Go back to Potassium Binding Sites List in 6uo2
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:26.1
occ:1.00
 O B:HOH636 2.7 18.5 1.0
O B:VAL247 2.7 21.3 1.0
O B:PHE241 2.7 19.7 1.0
O B:TYR280 2.9 15.3 1.0
O B:HOH653 3.0 17.2 1.0
O B:ASP244 3.0 19.2 1.0
C B:PHE241 3.6 16.6 1.0
CB B:PHE241 3.6 17.0 1.0
C B:TYR280 3.7 16.7 1.0
CB B:TYR280 3.8 18.6 1.0
C B:VAL247 3.9 17.0 1.0
C B:ASP244 4.1 18.4 1.0
CA B:PHE241 4.3 16.9 1.0
CA B:TYR280 4.4 17.6 1.0
N B:ASN281 4.4 18.0 1.0
N B:TYR249 4.4 13.2 1.0
N B:ASP244 4.5 22.0 1.0
N B:GLU242 4.6 17.8 1.0
CA B:LEU248 4.6 16.4 1.0
CA B:GLU242 4.7 15.8 1.0
O B:GLU242 4.7 22.5 1.0
N B:LEU248 4.7 15.1 1.0
CB B:ASN281 4.7 15.0 1.0
CA B:ASN281 4.7 17.5 1.0
C B:GLU242 4.7 21.0 1.0
CA B:ASP244 4.8 20.9 1.0
CB B:TYR249 4.8 12.3 1.0
CG B:PHE241 4.8 18.5 1.0
CB B:ASP244 4.9 20.4 1.0
CA B:VAL247 4.9 14.2 1.0
O B:GLY277 5.0 21.9 1.0
C B:LEU248 5.0 15.2 1.0
OD1 B:ASN281 5.0 19.1 1.0

Potassium binding site 4 out of 4 in 6uo2

Go back to Potassium Binding Sites List in 6uo2
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:18.7
occ:1.00
 O B:ASP230 2.6 16.5 1.0
O B:HIS232 2.7 17.9 1.0
OD1 B:ASP228 2.8 14.9 1.0
OG B:SER251 2.8 14.6 1.0
O B:VAL252 2.8 16.2 1.0
O B:ASP228 2.8 15.6 1.0
CG B:ASP228 3.3 14.6 1.0
C B:ASP228 3.5 15.3 1.0
C B:ASP230 3.6 14.9 1.0
C B:VAL252 3.7 15.0 1.0
C B:HIS232 3.7 20.3 1.0
N B:ASP230 3.8 16.0 1.0
CB B:ASP228 3.8 13.9 1.0
N B:VAL252 3.9 16.8 1.0
OD2 B:ASP228 3.9 15.1 1.0
CB B:HIS253 3.9 14.2 1.0
CB B:SER251 4.0 16.0 1.0
CA B:ASP230 4.1 14.6 1.0
N B:TRP229 4.2 13.8 1.0
C B:TRP229 4.2 17.4 1.0
CB B:ASP230 4.2 13.9 1.0
CA B:SER251 4.2 12.8 1.0
CA B:ASP228 4.3 16.4 1.0
ND1 B:HIS253 4.3 17.2 1.0
CA B:HIS233 4.3 15.9 1.0
CA B:TRP229 4.3 14.2 1.0
C B:SER251 4.4 18.8 1.0
N B:HIS233 4.4 16.3 1.0
N B:HIS232 4.5 15.9 1.0
CA B:HIS253 4.5 14.6 1.0
CA B:VAL252 4.5 16.4 1.0
N B:GLY234 4.5 17.2 1.0
N B:HIS253 4.5 15.1 1.0
CG B:HIS253 4.6 18.4 1.0
C B:VAL231 4.7 19.8 1.0
N B:VAL231 4.7 17.3 1.0
O B:HOH615 4.7 20.4 1.0
CA B:HIS232 4.7 18.1 1.0
OH B:TYR249 4.8 15.2 1.0
C B:HIS233 4.9 21.7 1.0
CE1 B:HIS192 4.9 14.8 1.0
O B:TRP229 4.9 16.2 1.0

Reference:

J.D.Osko, D.W.Christianson. Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31755702
DOI: 10.1021/ACS.BIOCHEM.9B00934
Page generated: Mon Aug 12 17:50:29 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy