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Potassium in PDB 6dvl: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115, PDB code: 6dvl was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.21 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.982, 82.601, 88.910, 90.00, 98.49, 90.00
R / Rfree (%) 17.6 / 20.3

Other elements in 6dvl:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115 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 in Complex with Ddk-115 (pdb code 6dvl). 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 in Complex with Ddk-115, PDB code: 6dvl:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6dvl

Go back to Potassium Binding Sites List in 6dvl
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115


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 in Complex with Ddk-115 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:4.5
occ:1.00
 O A:ASP612 2.6 5.0 1.0
O A:LEU634 2.7 5.5 1.0
O A:HIS614 2.7 4.0 1.0
OG A:SER633 2.8 4.9 1.0
O A:ASP610 2.9 3.2 1.0
OD1 A:ASP610 2.9 5.8 1.0
CG A:ASP610 3.2 10.5 1.0
C A:ASP610 3.5 7.1 1.0
C A:ASP612 3.6 7.7 1.0
C A:LEU634 3.7 6.3 1.0
C A:HIS614 3.7 5.1 1.0
CB A:ASP610 3.7 7.3 1.0
OD2 A:ASP610 3.8 12.5 1.0
N A:ASP612 3.8 5.6 1.0
CB A:HIS635 3.9 5.3 1.0
N A:LEU634 4.0 4.3 1.0
CB A:SER633 4.0 5.4 1.0
CA A:ASP612 4.1 4.7 1.0
N A:TRP611 4.2 5.9 1.0
C A:TRP611 4.2 6.0 1.0
CA A:ASP610 4.2 6.0 1.0
CB A:ASP612 4.2 4.5 1.0
CA A:HIS615 4.3 4.8 1.0
CA A:SER633 4.3 5.5 1.0
N A:HIS615 4.4 4.9 1.0
CA A:TRP611 4.4 5.3 1.0
ND1 A:HIS635 4.4 6.7 1.0
CA A:HIS635 4.4 6.1 1.0
N A:HIS614 4.4 3.4 1.0
N A:HIS635 4.4 5.6 1.0
C A:SER633 4.5 5.5 1.0
N A:GLY616 4.5 4.9 1.0
CA A:LEU634 4.5 6.8 1.0
O A:HOH922 4.6 11.7 1.0
CG A:HIS635 4.6 5.6 1.0
OH A:TYR631 4.7 9.0 1.0
CA A:HIS614 4.7 5.5 1.0
C A:VAL613 4.7 6.2 1.0
N A:VAL613 4.7 5.4 1.0
C A:HIS615 4.8 6.1 1.0
CE1 A:HIS573 4.9 6.9 1.0
O A:TRP611 5.0 6.2 1.0

Potassium binding site 2 out of 4 in 6dvl

Go back to Potassium Binding Sites List in 6dvl
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115


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 in Complex with Ddk-115 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:6.5
occ:1.00
 O A:PHE623 2.6 9.6 1.0
O A:VAL629 2.7 6.6 1.0
O A:TYR662 2.8 7.3 1.0
O A:HOH969 2.8 6.8 1.0
O A:ASP626 2.9 13.1 1.0
O A:HOH982 3.1 6.6 1.0
CB A:TYR662 3.6 7.9 1.0
C A:TYR662 3.6 9.9 1.0
C A:PHE623 3.6 7.3 1.0
CB A:PHE623 3.8 6.9 1.0
C A:VAL629 3.9 7.8 1.0
C A:ASP626 4.1 13.2 1.0
CA A:TYR662 4.2 9.0 1.0
CA A:PHE623 4.3 7.0 1.0
N A:TYR631 4.3 5.8 1.0
N A:ASN663 4.4 5.1 1.0
N A:ASP626 4.5 10.4 1.0
CA A:LEU630 4.5 6.5 1.0
N A:GLU624 4.6 9.1 1.0
CA A:GLU624 4.6 12.8 1.0
CA A:ASP626 4.7 9.0 1.0
O A:GLU624 4.7 9.3 1.0
N A:LEU630 4.7 4.8 1.0
C A:GLU624 4.7 10.3 1.0
CB A:ASP626 4.7 11.5 1.0
CB A:ASN663 4.8 6.5 1.0
CA A:ASN663 4.8 6.7 1.0
CB A:TYR631 4.8 4.0 1.0
O A:GLY659 4.9 9.0 1.0
CG A:TYR662 4.9 8.7 1.0
C A:LEU630 4.9 5.3 1.0
CA A:VAL629 4.9 5.8 1.0

Potassium binding site 3 out of 4 in 6dvl

Go back to Potassium Binding Sites List in 6dvl
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115


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 in Complex with Ddk-115 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:9.6
occ:1.00
 O B:ASP612 2.6 8.2 1.0
O B:LEU634 2.7 13.0 1.0
OG B:SER633 2.8 11.3 1.0
O B:HIS614 2.8 7.7 1.0
O B:ASP610 2.8 10.7 1.0
OD1 B:ASP610 2.9 15.8 1.0
CG B:ASP610 3.3 14.7 1.0
C B:ASP610 3.5 10.9 1.0
C B:ASP612 3.6 13.3 1.0
C B:LEU634 3.7 13.4 1.0
CB B:ASP610 3.7 9.4 1.0
C B:HIS614 3.8 9.5 1.0
N B:ASP612 3.8 11.9 1.0
N B:LEU634 3.9 15.3 1.0
CB B:HIS635 3.9 12.5 1.0
CB B:SER633 4.0 13.7 1.0
OD2 B:ASP610 4.0 11.2 1.0
CA B:ASP612 4.1 10.1 1.0
CA B:ASP610 4.2 10.2 1.0
N B:TRP611 4.2 12.9 1.0
C B:TRP611 4.2 13.7 1.0
CB B:ASP612 4.3 9.9 1.0
CA B:HIS615 4.3 9.9 1.0
CA B:SER633 4.3 13.7 1.0
CA B:TRP611 4.4 10.6 1.0
N B:HIS615 4.4 13.8 1.0
C B:SER633 4.4 12.0 1.0
N B:GLY616 4.4 11.6 1.0
CA B:HIS635 4.4 11.3 1.0
CA B:LEU634 4.5 11.2 1.0
N B:HIS635 4.5 11.2 1.0
ND1 B:HIS635 4.5 14.0 1.0
N B:HIS614 4.5 9.0 1.0
O B:HOH911 4.6 16.4 1.0
OH B:TYR631 4.7 12.6 1.0
CG B:HIS635 4.7 15.2 1.0
C B:HIS615 4.7 10.9 1.0
N B:VAL613 4.7 10.2 1.0
C B:VAL613 4.8 10.9 1.0
CA B:HIS614 4.8 12.7 1.0
CE1 B:HIS573 4.9 13.2 1.0
ND1 B:HIS573 5.0 13.4 1.0

Potassium binding site 4 out of 4 in 6dvl

Go back to Potassium Binding Sites List in 6dvl
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115


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 in Complex with Ddk-115 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:15.2
occ:1.00
 O B:PHE623 2.7 16.8 1.0
O B:VAL629 2.7 11.0 1.0
O B:HOH952 2.8 11.8 1.0
O B:TYR662 2.8 12.1 1.0
O B:ASP626 2.9 21.2 1.0
O B:HOH964 3.0 15.0 1.0
CB B:TYR662 3.6 15.9 1.0
C B:TYR662 3.6 17.3 1.0
C B:PHE623 3.6 14.4 1.0
CB B:PHE623 3.8 13.5 1.0
C B:VAL629 3.9 11.4 1.0
C B:ASP626 4.1 15.8 1.0
CA B:TYR662 4.3 17.5 1.0
N B:TYR631 4.3 14.6 1.0
CA B:PHE623 4.4 12.5 1.0
N B:ASN663 4.5 16.2 1.0
N B:ASP626 4.5 15.2 1.0
N B:GLU624 4.5 13.9 1.0
CA B:GLU624 4.5 18.1 1.0
CA B:LEU630 4.5 12.1 1.0
CA B:ASP626 4.7 14.7 1.0
O B:GLU624 4.7 16.2 1.0
C B:GLU624 4.7 15.4 1.0
N B:LEU630 4.7 8.9 1.0
CB B:ASP626 4.7 19.7 1.0
CB B:TYR631 4.8 10.7 1.0
CB B:ASN663 4.8 15.0 1.0
CA B:ASN663 4.8 16.3 1.0
O B:GLY659 4.8 17.6 1.0
C B:LEU630 4.9 13.7 1.0
CG B:TYR662 4.9 17.1 1.0
CA B:VAL629 5.0 10.3 1.0

Reference:

N.J.Porter, J.D.Osko, D.Diedrich, T.Kurz, J.M.Hooker, F.K.Hansen, D.W.Christianson. Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. J. Med. Chem. V. 61 8054 2018.
ISSN: ISSN 1520-4804
PubMed: 30118224
DOI: 10.1021/ACS.JMEDCHEM.8B01013
Page generated: Mon Aug 12 15:54:37 2024

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