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Potassium in PDB 6dvm: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122, PDB code: 6dvm 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) 56.42 / 1.47
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.450, 95.180, 98.030, 90.00, 98.87, 90.00
R / Rfree (%) 14.8 / 17

Other elements in 6dvm:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 also contains other interesting chemical elements:

Zinc (Zn) 4 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-122 (pdb code 6dvm). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122, PDB code: 6dvm:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6dvm

Go back to Potassium Binding Sites List in 6dvm
Potassium binding site 1 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


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-122 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:7.9
occ:1.00
 O A:ASP612 2.6 8.5 1.0
O A:LEU634 2.7 8.4 1.0
O A:HIS614 2.7 5.9 1.0
OD1 A:ASP610 2.7 8.6 1.0
O A:ASP610 2.8 7.8 1.0
OG A:SER633 2.8 8.0 1.0
CG A:ASP610 3.2 6.2 1.0
C A:ASP610 3.5 6.6 1.0
C A:ASP612 3.6 8.0 1.0
C A:LEU634 3.7 9.4 1.0
C A:HIS614 3.7 6.6 1.0
N A:ASP612 3.8 7.6 1.0
CB A:ASP610 3.8 7.0 1.0
N A:LEU634 3.9 7.9 1.0
OD2 A:ASP610 3.9 8.9 1.0
CB A:SER633 4.0 7.4 1.0
CB A:HIS635 4.0 8.9 1.0
CA A:ASP612 4.1 5.9 1.0
C A:TRP611 4.2 8.0 1.0
N A:TRP611 4.2 6.8 1.0
CB A:ASP612 4.2 8.2 1.0
CA A:ASP610 4.3 6.6 1.0
CA A:HIS615 4.3 6.1 1.0
CA A:SER633 4.3 7.4 1.0
ND1 A:HIS635 4.4 8.6 1.0
CA A:TRP611 4.4 7.1 1.0
N A:HIS615 4.4 7.0 1.0
N A:HIS614 4.4 6.9 1.0
CA A:HIS635 4.4 6.1 1.0
C A:SER633 4.5 7.7 1.0
CA A:LEU634 4.5 7.6 1.0
O A:HOH924 4.5 10.9 1.0
N A:GLY616 4.5 5.7 1.0
N A:HIS635 4.5 6.8 1.0
CG A:HIS635 4.7 7.8 1.0
C A:VAL613 4.7 6.2 1.0
CA A:HIS614 4.7 5.2 1.0
N A:VAL613 4.7 6.0 1.0
OH A:TYR631 4.7 8.6 1.0
CE1 A:HIS573 4.7 7.7 1.0
C A:HIS615 4.8 6.4 1.0
O A:TRP611 4.9 8.3 1.0
ND1 A:HIS573 4.9 7.8 1.0

Potassium binding site 2 out of 8 in 6dvm

Go back to Potassium Binding Sites List in 6dvm
Potassium binding site 2 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


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-122 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:11.1
occ:1.00
 O A:VAL629 2.7 10.3 1.0
O A:PHE623 2.7 11.4 1.0
O A:HOH1064 2.7 12.4 1.0
O A:TYR662 2.8 10.7 1.0
O A:ASP626 2.9 14.2 1.0
O A:HOH1041 3.0 9.1 1.0
C A:TYR662 3.6 14.5 1.0
CB A:TYR662 3.6 12.7 1.0
C A:PHE623 3.6 10.2 1.0
CB A:PHE623 3.7 10.8 1.0
C A:VAL629 3.9 8.4 1.0
C A:ASP626 4.1 13.3 1.0
CA A:TYR662 4.2 11.3 1.0
CA A:PHE623 4.3 7.9 1.0
N A:TYR631 4.3 9.6 1.0
N A:ASN663 4.4 11.1 1.0
N A:ASP626 4.5 11.4 1.0
CA A:LEU630 4.5 8.8 1.0
N A:GLU624 4.6 9.4 1.0
CA A:GLU624 4.6 13.6 1.0
CA A:ASP626 4.6 11.3 1.0
CB A:ASP626 4.7 11.1 1.0
N A:LEU630 4.7 9.0 1.0
C A:GLU624 4.7 13.6 1.0
O A:GLU624 4.7 10.6 1.0
CB A:TYR631 4.7 6.7 1.0
CA A:ASN663 4.8 10.6 1.0
CB A:ASN663 4.9 10.3 1.0
C A:LEU630 4.9 11.2 1.0
O A:GLY659 4.9 12.3 1.0
CG A:TYR662 4.9 12.3 1.0
CA A:VAL629 4.9 8.9 1.0
CG A:PHE623 5.0 8.4 1.0

Potassium binding site 3 out of 8 in 6dvm

Go back to Potassium Binding Sites List in 6dvm
Potassium binding site 3 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


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-122 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:5.9
occ:1.00
 O B:ASP612 2.6 5.8 1.0
O B:LEU634 2.7 6.1 1.0
O B:HIS614 2.7 5.0 1.0
OD1 B:ASP610 2.7 7.1 1.0
OG B:SER633 2.8 5.9 1.0
O B:ASP610 2.9 5.5 1.0
CG B:ASP610 3.3 4.8 1.0
C B:ASP610 3.5 5.7 1.0
C B:ASP612 3.6 4.4 1.0
C B:HIS614 3.7 5.2 1.0
C B:LEU634 3.7 5.9 1.0
N B:ASP612 3.8 5.1 1.0
CB B:ASP610 3.8 4.9 1.0
N B:LEU634 3.9 5.8 1.0
OD2 B:ASP610 3.9 6.4 1.0
CB B:SER633 4.0 5.5 1.0
CB B:HIS635 4.0 6.3 1.0
CA B:ASP612 4.1 4.7 1.0
N B:TRP611 4.2 4.6 1.0
C B:TRP611 4.2 5.6 1.0
CB B:ASP612 4.2 6.2 1.0
CA B:ASP610 4.3 6.0 1.0
CA B:HIS615 4.3 4.5 1.0
CA B:TRP611 4.3 5.6 1.0
CA B:SER633 4.3 6.3 1.0
N B:HIS615 4.3 5.0 1.0
ND1 B:HIS635 4.4 7.0 1.0
N B:HIS614 4.4 4.6 1.0
CA B:HIS635 4.5 6.1 1.0
N B:GLY616 4.5 5.6 1.0
C B:SER633 4.5 5.8 1.0
CA B:LEU634 4.5 6.6 1.0
N B:HIS635 4.6 6.1 1.0
O B:HOH915 4.6 7.4 1.0
C B:VAL613 4.7 6.3 1.0
CG B:HIS635 4.7 4.8 1.0
CA B:HIS614 4.7 5.3 1.0
CE1 B:HIS573 4.7 6.4 1.0
OH B:TYR631 4.7 7.1 1.0
N B:VAL613 4.7 4.6 1.0
C B:HIS615 4.8 4.4 1.0
ND1 B:HIS573 4.9 4.6 1.0
O B:TRP611 4.9 5.3 1.0

Potassium binding site 4 out of 8 in 6dvm

Go back to Potassium Binding Sites List in 6dvm
Potassium binding site 4 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


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-122 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:8.8
occ:1.00
 O B:PHE623 2.6 7.2 1.0
O B:VAL629 2.7 10.1 1.0
O B:HOH1071 2.7 10.3 1.0
O B:TYR662 2.8 7.5 1.0
O B:ASP626 2.9 12.3 1.0
O B:HOH1078 3.0 7.1 1.0
C B:TYR662 3.6 7.3 1.0
CB B:TYR662 3.6 9.7 1.0
C B:PHE623 3.6 6.0 1.0
CB B:PHE623 3.7 6.7 1.0
C B:VAL629 3.9 8.4 1.0
C B:ASP626 4.1 11.9 1.0
CA B:TYR662 4.2 7.7 1.0
CA B:PHE623 4.3 5.7 1.0
N B:TYR631 4.3 6.8 1.0
N B:ASN663 4.4 7.7 1.0
N B:ASP626 4.5 9.9 1.0
N B:GLU624 4.5 6.9 1.0
CA B:LEU630 4.5 6.2 1.0
CB B:ASP626 4.6 9.0 1.0
CA B:GLU624 4.6 7.5 1.0
CA B:ASP626 4.6 9.6 1.0
N B:LEU630 4.7 6.0 1.0
C B:GLU624 4.7 10.4 1.0
O B:GLU624 4.7 9.3 1.0
CB B:TYR631 4.8 6.3 1.0
CA B:ASN663 4.8 6.3 1.0
CB B:ASN663 4.8 6.5 1.0
C B:LEU630 4.9 7.7 1.0
CG B:TYR662 4.9 11.0 1.0
O B:GLY659 4.9 10.4 1.0
CA B:VAL629 4.9 7.2 1.0
CG B:PHE623 5.0 6.0 1.0

Potassium binding site 5 out of 8 in 6dvm

Go back to Potassium Binding Sites List in 6dvm
Potassium binding site 5 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K802

b:5.7
occ:1.00
 O C:ASP612 2.6 6.5 1.0
O C:LEU634 2.7 6.6 1.0
O C:HIS614 2.7 6.4 1.0
OG C:SER633 2.8 5.7 1.0
OD1 C:ASP610 2.8 5.6 1.0
O C:ASP610 2.9 5.9 1.0
CG C:ASP610 3.3 7.2 1.0
C C:ASP610 3.5 6.2 1.0
C C:ASP612 3.6 5.8 1.0
C C:HIS614 3.7 5.8 1.0
C C:LEU634 3.7 7.3 1.0
N C:ASP612 3.8 5.2 1.0
CB C:ASP610 3.8 6.1 1.0
N C:LEU634 3.8 5.8 1.0
OD2 C:ASP610 3.9 8.0 1.0
CB C:SER633 4.0 4.2 1.0
CB C:HIS635 4.0 6.5 1.0
CA C:ASP612 4.1 4.5 1.0
CB C:ASP612 4.2 5.0 1.0
C C:TRP611 4.2 6.1 1.0
N C:TRP611 4.2 4.6 1.0
CA C:HIS615 4.3 5.5 1.0
CA C:ASP610 4.3 5.9 1.0
CA C:SER633 4.3 3.6 1.0
N C:HIS615 4.4 5.5 1.0
CA C:TRP611 4.4 4.4 1.0
ND1 C:HIS635 4.4 6.0 1.0
N C:HIS614 4.4 6.5 1.0
C C:SER633 4.5 6.4 1.0
CA C:HIS635 4.5 5.8 1.0
CA C:LEU634 4.5 6.7 1.0
N C:GLY616 4.5 5.8 1.0
O C:HOH934 4.6 7.3 1.0
N C:HIS635 4.6 6.0 1.0
C C:VAL613 4.7 5.8 1.0
CG C:HIS635 4.7 5.0 1.0
CA C:HIS614 4.7 4.7 1.0
CE1 C:HIS573 4.7 5.9 1.0
OH C:TYR631 4.7 7.2 1.0
N C:VAL613 4.7 4.7 1.0
C C:HIS615 4.8 4.5 1.0
ND1 C:HIS573 4.9 5.7 1.0
O C:TRP611 4.9 6.1 1.0

Potassium binding site 6 out of 8 in 6dvm

Go back to Potassium Binding Sites List in 6dvm
Potassium binding site 6 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K803

b:8.6
occ:1.00
 O C:VAL629 2.7 8.0 1.0
O C:PHE623 2.7 6.3 1.0
O C:HOH1017 2.7 7.8 1.0
O C:TYR662 2.9 6.0 1.0
O C:ASP626 2.9 10.7 1.0
O C:HOH1073 3.0 8.4 1.0
C C:TYR662 3.6 7.1 1.0
C C:PHE623 3.6 7.5 1.0
CB C:TYR662 3.7 8.8 1.0
CB C:PHE623 3.7 7.2 1.0
C C:VAL629 3.9 5.9 1.0
C C:ASP626 4.1 9.7 1.0
CA C:TYR662 4.2 7.0 1.0
N C:TYR631 4.3 5.8 1.0
CA C:PHE623 4.3 6.2 1.0
N C:ASN663 4.4 6.6 1.0
N C:ASP626 4.5 8.0 1.0
CA C:LEU630 4.5 6.0 1.0
N C:GLU624 4.5 7.5 1.0
CA C:GLU624 4.6 8.0 1.0
CB C:ASP626 4.6 9.1 1.0
CA C:ASP626 4.7 9.2 1.0
N C:LEU630 4.7 5.1 1.0
C C:GLU624 4.7 6.9 1.0
CB C:TYR631 4.7 6.0 1.0
O C:GLU624 4.7 7.5 1.0
CA C:ASN663 4.8 6.1 1.0
CB C:ASN663 4.8 5.3 1.0
C C:LEU630 4.8 6.4 1.0
O C:GLY659 4.9 8.6 1.0
CA C:VAL629 5.0 6.5 1.0
CG C:TYR662 5.0 9.4 1.0
CG C:PHE623 5.0 6.1 1.0

Potassium binding site 7 out of 8 in 6dvm

Go back to Potassium Binding Sites List in 6dvm
Potassium binding site 7 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K802

b:5.6
occ:1.00
 O D:ASP612 2.6 5.3 1.0
O D:HIS614 2.7 5.4 1.0
O D:LEU634 2.7 5.3 1.0
OG D:SER633 2.8 5.8 1.0
OD1 D:ASP610 2.8 6.6 1.0
O D:ASP610 2.8 4.8 1.0
CG D:ASP610 3.3 6.2 1.0
C D:ASP610 3.5 5.3 1.0
C D:ASP612 3.6 4.0 1.0
C D:HIS614 3.7 5.1 1.0
C D:LEU634 3.7 7.1 1.0
N D:ASP612 3.9 4.6 1.0
CB D:ASP610 3.9 5.8 1.0
N D:LEU634 3.9 4.7 1.0
OD2 D:ASP610 3.9 7.0 1.0
CB D:SER633 3.9 4.6 1.0
CB D:HIS635 4.0 5.4 1.0
CA D:ASP612 4.2 5.4 1.0
N D:TRP611 4.2 4.3 1.0
C D:TRP611 4.2 5.2 1.0
CB D:ASP612 4.3 5.2 1.0
CA D:ASP610 4.3 3.8 1.0
CA D:SER633 4.3 4.4 1.0
CA D:HIS615 4.3 4.5 1.0
CA D:TRP611 4.3 5.3 1.0
N D:HIS615 4.3 4.7 1.0
ND1 D:HIS635 4.4 5.3 1.0
N D:HIS614 4.4 5.3 1.0
C D:SER633 4.5 6.5 1.0
CA D:HIS635 4.5 4.5 1.0
O D:HOH948 4.5 7.7 1.0
CA D:LEU634 4.5 6.7 1.0
N D:GLY616 4.5 4.5 1.0
N D:HIS635 4.6 7.0 1.0
CG D:HIS635 4.6 5.1 1.0
C D:VAL613 4.7 7.0 1.0
CA D:HIS614 4.7 5.0 1.0
CE1 D:HIS573 4.7 6.4 1.0
OH D:TYR631 4.7 6.1 1.0
N D:VAL613 4.8 4.0 1.0
C D:HIS615 4.8 4.6 1.0
O D:TRP611 4.9 5.3 1.0
ND1 D:HIS573 4.9 6.2 1.0

Potassium binding site 8 out of 8 in 6dvm

Go back to Potassium Binding Sites List in 6dvm
Potassium binding site 8 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-122 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K803

b:7.0
occ:1.00
 O D:HOH1003 2.6 7.7 1.0
O D:VAL629 2.7 7.6 1.0
O D:PHE623 2.7 6.5 1.0
O D:TYR662 2.8 5.3 1.0
O D:ASP626 2.9 10.0 1.0
O D:HOH1111 2.9 6.6 1.0
C D:TYR662 3.6 6.0 1.0
CB D:TYR662 3.6 6.4 1.0
C D:PHE623 3.6 5.8 1.0
CB D:PHE623 3.7 5.7 1.0
C D:VAL629 3.9 6.6 1.0
C D:ASP626 4.1 9.5 1.0
CA D:TYR662 4.2 7.4 1.0
CA D:PHE623 4.3 4.7 1.0
N D:TYR631 4.3 4.9 1.0
N D:ASN663 4.4 4.8 1.0
N D:ASP626 4.5 8.6 1.0
N D:GLU624 4.5 6.5 1.0
CA D:LEU630 4.6 4.1 1.0
CA D:GLU624 4.6 7.2 1.0
CB D:ASP626 4.6 8.7 1.0
CA D:ASP626 4.6 6.8 1.0
N D:LEU630 4.7 5.0 1.0
C D:GLU624 4.7 7.4 1.0
O D:GLU624 4.7 7.5 1.0
CB D:TYR631 4.7 6.1 1.0
CA D:ASN663 4.8 4.8 1.0
CB D:ASN663 4.9 5.7 1.0
O D:GLY659 4.9 8.2 1.0
C D:LEU630 4.9 4.7 1.0
CA D:VAL629 4.9 4.9 1.0
CG D:TYR662 4.9 6.2 1.0
CG D:PHE623 5.0 5.6 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 Dec 14 00:34:45 2020

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