Atomistry » Potassium » PDB 6u9t-6v7h » 6v79
Atomistry »
  Potassium »
    PDB 6u9t-6v7h »
      6v79 »

Potassium in PDB 6v79: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376, PDB code: 6v79 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) 74.34 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.252, 108.135, 74.345, 90.00, 90.01, 90.00
R / Rfree (%) 19.5 / 23.4

Other elements in 6v79:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376 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 2 (CD2) Complexed with NF2376 (pdb code 6v79). 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 2 (CD2) Complexed with NF2376, PDB code: 6v79:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6v79

Go back to Potassium Binding Sites List in 6v79
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376


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 2 (CD2) Complexed with NF2376 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:21.2
occ:1.00
 O A:ASP612 2.6 18.1 1.0
O A:LEU634 2.7 21.9 1.0
OD1 A:ASP610 2.7 17.7 1.0
O A:HIS614 2.7 18.0 1.0
OG A:SER633 2.8 16.1 1.0
O A:ASP610 2.9 21.3 1.0
CG A:ASP610 3.3 18.8 1.0
C A:ASP610 3.6 21.3 1.0
C A:ASP612 3.6 21.6 1.0
C A:HIS614 3.7 19.6 1.0
C A:LEU634 3.7 19.4 1.0
CB A:ASP610 3.8 19.3 1.0
N A:ASP612 3.8 14.8 1.0
CB A:SER633 3.9 17.1 1.0
N A:LEU634 3.9 16.6 1.0
CB A:HIS635 3.9 16.5 1.0
OD2 A:ASP610 4.0 16.4 1.0
CA A:ASP612 4.1 19.9 1.0
CB A:ASP612 4.2 17.5 1.0
CA A:HIS615 4.2 17.6 1.0
N A:TRP611 4.3 16.6 1.0
CA A:ASP610 4.3 18.2 1.0
C A:TRP611 4.3 17.9 1.0
CA A:SER633 4.3 20.4 1.0
N A:HIS615 4.3 17.5 1.0
CA A:TRP611 4.4 16.1 1.0
ND1 A:HIS635 4.4 15.7 1.0
N A:HIS614 4.4 17.9 1.0
CA A:HIS635 4.4 18.4 1.0
N A:GLY616 4.4 22.3 1.0
C A:SER633 4.5 16.4 1.0
CA A:LEU634 4.5 18.6 1.0
N A:HIS635 4.5 16.7 1.0
O A:HOH911 4.6 17.5 1.0
CG A:HIS635 4.6 18.3 1.0
OH A:TYR631 4.7 20.1 1.0
C A:VAL613 4.7 17.6 1.0
C A:HIS615 4.7 24.4 1.0
CA A:HIS614 4.7 18.4 1.0
N A:VAL613 4.7 20.1 1.0
CE1 A:HIS573 4.9 22.8 1.0
ND1 A:HIS573 5.0 23.9 1.0

Potassium binding site 2 out of 4 in 6v79

Go back to Potassium Binding Sites List in 6v79
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376


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 2 (CD2) Complexed with NF2376 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:32.2
occ:1.00
 O A:PHE623 2.7 21.9 1.0
O A:TYR662 2.7 16.6 1.0
O A:VAL629 2.8 18.3 1.0
O A:HOH931 2.8 18.2 1.0
O A:ASP626 2.9 28.6 1.0
O A:HOH921 3.1 19.3 1.0
C A:TYR662 3.5 19.6 1.0
CB A:TYR662 3.6 16.7 1.0
C A:PHE623 3.7 22.3 1.0
CB A:PHE623 3.8 18.8 1.0
C A:VAL629 4.0 22.2 1.0
C A:ASP626 4.1 24.1 1.0
CA A:TYR662 4.2 18.9 1.0
N A:ASN663 4.3 21.9 1.0
N A:TYR631 4.3 13.6 1.0
CA A:PHE623 4.4 20.3 1.0
N A:ASP626 4.5 20.8 1.0
N A:GLU624 4.5 23.1 1.0
CA A:GLU624 4.6 22.0 1.0
CA A:ASN663 4.6 18.4 1.0
CB A:ASN663 4.6 15.7 1.0
CA A:LEU630 4.6 17.0 1.0
O A:GLU624 4.7 22.2 1.0
CA A:ASP626 4.7 23.6 1.0
CB A:ASP626 4.7 20.8 1.0
C A:GLU624 4.7 19.6 1.0
CB A:TYR631 4.8 15.9 1.0
O A:GLY659 4.8 22.2 1.0
N A:LEU630 4.8 16.7 1.0
OD1 A:ASN663 4.9 21.9 1.0
C A:LEU630 4.9 20.9 1.0
CG A:TYR662 5.0 24.3 1.0

Potassium binding site 3 out of 4 in 6v79

Go back to Potassium Binding Sites List in 6v79
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376


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 2 (CD2) Complexed with NF2376 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:19.0
occ:1.00
 O B:ASP612 2.7 19.8 1.0
O B:HIS614 2.7 20.3 1.0
O B:LEU634 2.7 20.1 1.0
OD1 B:ASP610 2.8 18.8 1.0
OG B:SER633 2.8 15.4 1.0
O B:ASP610 2.8 20.3 1.0
CG B:ASP610 3.2 19.1 1.0
C B:ASP610 3.5 18.8 1.0
C B:HIS614 3.7 20.7 1.0
C B:LEU634 3.7 17.8 1.0
C B:ASP612 3.7 21.4 1.0
CB B:ASP610 3.8 16.0 1.0
CB B:HIS635 3.9 18.8 1.0
N B:ASP612 3.9 22.2 1.0
OD2 B:ASP610 3.9 16.5 1.0
N B:LEU634 3.9 12.7 1.0
CB B:SER633 4.0 21.8 1.0
N B:TRP611 4.1 20.5 1.0
CA B:ASP612 4.2 19.3 1.0
CA B:ASP610 4.2 17.4 1.0
CA B:HIS615 4.2 22.2 1.0
C B:TRP611 4.2 18.2 1.0
CB B:ASP612 4.3 16.6 1.0
N B:HIS615 4.3 21.5 1.0
CA B:TRP611 4.3 16.4 1.0
CA B:SER633 4.3 17.5 1.0
N B:HIS614 4.4 19.3 1.0
ND1 B:HIS635 4.4 22.6 1.0
CA B:HIS635 4.4 19.5 1.0
CA B:LEU634 4.5 18.9 1.0
N B:GLY616 4.5 21.1 1.0
N B:HIS635 4.5 19.9 1.0
O B:HOH924 4.5 16.3 1.0
C B:SER633 4.5 22.3 1.0
OH B:TYR631 4.5 17.0 1.0
CG B:HIS635 4.6 18.0 1.0
CA B:HIS614 4.7 20.7 1.0
C B:VAL613 4.7 22.6 1.0
C B:HIS615 4.7 22.4 1.0
N B:VAL613 4.8 20.9 1.0
CE1 B:HIS573 4.9 26.2 1.0
ND1 B:HIS573 5.0 24.2 1.0
O B:TRP611 5.0 19.1 1.0

Potassium binding site 4 out of 4 in 6v79

Go back to Potassium Binding Sites List in 6v79
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376


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 2 (CD2) Complexed with NF2376 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:28.7
occ:1.00
 O B:TYR662 2.7 16.9 1.0
O B:HOH912 2.7 16.8 1.0
O B:PHE623 2.7 22.2 1.0
O B:VAL629 2.8 24.2 1.0
O B:ASP626 2.9 23.4 1.0
O B:HOH975 3.0 22.2 1.0
C B:TYR662 3.5 21.3 1.0
CB B:TYR662 3.6 18.7 1.0
C B:PHE623 3.7 21.7 1.0
CB B:PHE623 3.9 25.0 1.0
C B:VAL629 4.0 20.8 1.0
C B:ASP626 4.1 27.7 1.0
CA B:TYR662 4.2 18.6 1.0
N B:ASN663 4.2 17.9 1.0
N B:TYR631 4.4 11.2 1.0
CA B:PHE623 4.4 21.3 1.0
CA B:GLU624 4.5 20.6 1.0
N B:GLU624 4.5 20.5 1.0
N B:ASP626 4.6 25.7 1.0
CA B:LEU630 4.6 17.3 1.0
CA B:ASN663 4.6 16.6 1.0
C B:GLU624 4.6 22.4 1.0
O B:GLU624 4.7 20.8 1.0
CB B:ASN663 4.7 12.9 1.0
O B:GLY659 4.7 18.2 1.0
CA B:ASP626 4.7 20.9 1.0
N B:LEU630 4.8 20.8 1.0
CB B:ASP626 4.8 26.8 1.0
CB B:TYR631 4.8 20.8 1.0
C B:LEU630 5.0 20.9 1.0
CG B:TYR662 5.0 24.2 1.0

Reference:

J.D.Osko, D.W.Christianson. Harnessing An Epigenetic Approach to Idiopathic Pulmonary Fibrosis: Design, Synthesis, Structural Analysis, and Biological Evaluation of Selective HDAC6 Inhibitors To Be Published.
Page generated: Mon Aug 12 17:57:11 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy