Atomistry » Potassium » PDB 6ukn-6vwo » 6uoc
Atomistry »
  Potassium »
    PDB 6ukn-6vwo »
      6uoc »

Potassium in PDB 6uoc: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat, PDB code: 6uoc 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) 42.95 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.160, 60.400, 122.160, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 16.8

Other elements in 6uoc:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat (pdb code 6uoc). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat, PDB code: 6uoc:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6uoc

Go back to Potassium Binding Sites List in 6uoc
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat


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) K330L Mutant Complexed with Givinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:7.2
occ:0.91
O A:ASP230 2.6 7.7 1.0
O A:HIS232 2.7 8.3 1.0
OD1 A:ASP228 2.7 8.2 1.0
OG A:SER251 2.8 8.2 1.0
O A:VAL252 2.8 7.6 1.0
O A:ASP228 2.9 8.0 1.0
CG A:ASP228 3.2 8.9 1.0
C A:ASP228 3.5 7.9 1.0
C A:ASP230 3.6 7.1 1.0
C A:VAL252 3.7 8.5 1.0
C A:HIS232 3.7 7.5 1.0
OD2 A:ASP228 3.8 8.4 1.0
N A:ASP230 3.8 7.0 1.0
CB A:ASP228 3.8 7.7 1.0
N A:VAL252 3.9 7.0 1.0
CB A:SER251 3.9 8.6 1.0
CB A:HIS253 4.0 8.2 1.0
CA A:ASP230 4.1 6.7 1.0
C A:TRP229 4.2 8.2 1.0
N A:TRP229 4.2 7.2 1.0
CA A:SER251 4.2 7.9 1.0
CB A:ASP230 4.3 7.8 1.0
CA A:ASP228 4.3 6.7 1.0
ND1 A:HIS253 4.3 8.2 1.0
CA A:HIS233 4.3 7.4 1.0
CA A:TRP229 4.4 7.2 1.0
C A:SER251 4.4 8.2 1.0
N A:HIS233 4.4 6.8 1.0
N A:HIS232 4.4 6.8 1.0
CA A:HIS253 4.5 7.6 1.0
CA A:VAL252 4.5 8.1 1.0
N A:HIS253 4.5 7.8 1.0
N A:GLY234 4.6 6.8 1.0
CG A:HIS253 4.6 7.7 1.0
O A:HOH748 4.7 8.7 1.0
C A:VAL231 4.7 7.8 1.0
N A:VAL231 4.7 7.1 1.0
CA A:HIS232 4.7 6.5 1.0
OH A:TYR249 4.8 8.3 1.0
O A:TRP229 4.9 7.9 1.0
C A:HIS233 4.9 7.8 1.0
CE1 A:HIS192 4.9 9.7 1.0

Potassium binding site 2 out of 2 in 6uoc

Go back to Potassium Binding Sites List in 6uoc
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Givinostat


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) K330L Mutant Complexed with Givinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:10.8
occ:0.87
O A:VAL247 2.6 12.0 1.0
O A:HOH829 2.6 12.8 1.0
O A:PHE241 2.7 11.8 1.0
O A:TYR280 2.9 10.7 1.0
O A:ASP244 2.9 13.5 1.0
O A:HOH825 3.0 11.3 1.0
C A:PHE241 3.6 10.4 1.0
C A:TYR280 3.7 11.1 1.0
CB A:PHE241 3.7 11.4 1.0
CB A:TYR280 3.8 12.4 1.0
C A:VAL247 3.9 9.0 1.0
C A:ASP244 4.0 15.8 1.0
CA A:PHE241 4.3 9.9 1.0
CA A:TYR280 4.3 10.2 1.0
N A:TYR249 4.4 8.4 1.0
N A:ASP244 4.5 14.7 1.0
N A:ASN281 4.5 10.6 1.0
CA A:LEU248 4.5 9.2 0.3
CA A:LEU248 4.6 9.1 0.7
N A:GLU242 4.6 11.5 1.0
CA A:ASP244 4.6 13.6 1.0
N A:LEU248 4.6 8.5 0.3
N A:LEU248 4.7 8.5 0.7
CB A:ASP244 4.7 14.2 1.0
O A:GLU242 4.7 12.3 1.0
C A:GLU242 4.8 11.4 1.0
CB A:ASN281 4.8 9.9 1.0
CA A:ASN281 4.8 8.4 1.0
CA A:GLU242 4.8 12.0 1.0
CA A:VAL247 4.9 9.5 1.0
C A:LEU248 4.9 8.9 0.3
CB A:TYR249 4.9 9.5 1.0
CG A:PHE241 4.9 8.7 1.0
C A:LEU248 4.9 8.9 0.7
O A:GLY277 4.9 15.2 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 Dec 14 01:52:59 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy