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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

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