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Potassium in PDB 8d9a: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8, PDB code: 8d9a was solved by P.R.Watson, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.51 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.035, 92.044, 96.2, 90, 90, 90
R / Rfree (%) 18.3 / 21.7

Other elements in 8d9a:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Fluorine (F) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8 (pdb code 8d9a). 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 Complexed with Fluorinated Inhibitor 8, PDB code: 8d9a:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8d9a

Go back to Potassium Binding Sites List in 8d9a
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8


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 Complexed with Fluorinated Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:14.0
occ:1.00
 O A:ASP612 2.6 14.4 1.0
O A:LEU634 2.7 14.8 1.0
O A:HIS614 2.7 14.6 1.0
O A:ASP610 2.8 15.0 1.0
OD1 A:ASP610 2.8 14.2 1.0
OG A:SER633 2.8 14.3 1.0
CG A:ASP610 3.3 13.6 1.0
C A:ASP610 3.5 13.6 1.0
C A:ASP612 3.6 16.3 1.0
C A:HIS614 3.6 13.9 1.0
C A:LEU634 3.7 13.4 1.0
CB A:ASP610 3.8 14.2 1.0
N A:ASP612 3.9 11.3 1.0
OD2 A:ASP610 3.9 14.6 1.0
N A:LEU634 3.9 13.6 1.0
CB A:SER633 4.0 12.9 1.0
CB A:HIS635 4.0 15.7 1.0
CA A:ASP612 4.1 13.1 1.0
CA A:HIS615 4.2 9.9 1.0
N A:TRP611 4.2 11.5 1.0
C A:TRP611 4.2 14.9 1.0
CA A:ASP610 4.2 13.0 1.0
CB A:ASP612 4.2 16.1 1.0
N A:HIS615 4.3 13.7 1.0
CA A:SER633 4.3 13.1 1.0
CA A:TRP611 4.3 10.4 1.0
ND1 A:HIS635 4.4 14.3 1.0
N A:HIS614 4.4 13.6 1.0
N A:GLY616 4.4 14.5 1.0
CA A:LEU634 4.5 12.0 1.0
C A:SER633 4.5 16.6 1.0
O A:HOH924 4.5 15.8 1.0
CA A:HIS635 4.5 13.8 1.0
N A:HIS635 4.5 13.0 1.0
C A:VAL613 4.7 14.8 1.0
CG A:HIS635 4.7 16.1 1.0
CA A:HIS614 4.7 14.1 1.0
C A:HIS615 4.7 13.2 1.0
OH A:TYR631 4.7 11.4 1.0
N A:VAL613 4.7 12.6 1.0
O A:TRP611 4.9 14.3 1.0
CE1 A:HIS573 4.9 13.6 1.0
ND1 A:HIS573 5.0 13.7 1.0

Potassium binding site 2 out of 4 in 8d9a

Go back to Potassium Binding Sites List in 8d9a
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8


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 Complexed with Fluorinated Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K804

b:15.9
occ:1.00
 O A:PHE623 2.6 15.6 1.0
O A:VAL629 2.7 14.9 1.0
O A:HOH942 2.7 16.9 1.0
O A:TYR662 2.8 15.4 1.0
O A:ASP626 2.9 20.6 1.0
O A:HOH1008 3.1 16.2 1.0
C A:PHE623 3.6 15.1 1.0
C A:TYR662 3.6 19.9 1.0
CB A:TYR662 3.7 17.9 1.0
CB A:PHE623 3.7 13.3 1.0
C A:VAL629 3.9 14.1 1.0
C A:ASP626 4.0 16.9 1.0
CA A:PHE623 4.3 14.9 1.0
CA A:TYR662 4.3 17.3 1.0
N A:TYR631 4.4 12.1 1.0
N A:ASP626 4.4 20.5 1.0
N A:ASN663 4.4 15.7 1.0
CA A:ASP626 4.5 17.7 1.0
O A:GLU624 4.5 15.6 0.4
CB A:ASP626 4.5 22.1 1.0
N A:GLU624 4.6 16.5 0.4
CA A:LEU630 4.6 15.6 1.0
N A:GLU624 4.6 16.5 0.6
CA A:GLU624 4.7 17.0 0.6
C A:GLU624 4.7 16.6 0.4
N A:LEU630 4.7 13.4 1.0
CA A:GLU624 4.7 17.0 0.4
CB A:TYR631 4.7 12.0 1.0
C A:GLU624 4.8 16.6 0.6
CA A:ASN663 4.8 14.2 1.0
O A:GLU624 4.8 15.5 0.6
CB A:ASN663 4.8 14.8 1.0
O A:GLY659 4.9 20.7 1.0
C A:LEU630 4.9 15.6 1.0
CA A:VAL629 5.0 13.4 1.0
CG A:PHE623 5.0 14.4 1.0

Potassium binding site 3 out of 4 in 8d9a

Go back to Potassium Binding Sites List in 8d9a
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8


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 Complexed with Fluorinated Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:13.2
occ:1.00
 O B:ASP612 2.6 12.4 1.0
O B:LEU634 2.6 14.6 1.0
OG B:SER633 2.7 13.2 1.0
O B:HIS614 2.7 13.0 1.0
OD1 B:ASP610 2.8 12.6 1.0
O B:ASP610 2.9 12.3 1.0
CG B:ASP610 3.3 14.6 1.0
C B:ASP610 3.5 14.2 1.0
C B:ASP612 3.6 12.6 1.0
C B:LEU634 3.7 13.7 1.0
C B:HIS614 3.7 14.8 1.0
CB B:ASP610 3.8 12.5 1.0
N B:ASP612 3.9 12.1 1.0
CB B:SER633 3.9 12.3 1.0
N B:LEU634 3.9 13.4 1.0
OD2 B:ASP610 4.0 14.0 1.0
CB B:HIS635 4.0 15.6 1.0
CA B:ASP612 4.1 10.2 1.0
C B:TRP611 4.2 11.4 1.0
CB B:ASP612 4.2 13.6 1.0
N B:TRP611 4.2 11.6 1.0
CA B:HIS615 4.3 13.3 1.0
CA B:ASP610 4.3 11.9 1.0
CA B:SER633 4.3 13.0 1.0
CA B:TRP611 4.3 11.1 1.0
N B:HIS615 4.3 13.6 1.0
ND1 B:HIS635 4.4 14.6 1.0
N B:HIS614 4.4 13.0 1.0
N B:GLY616 4.4 11.3 1.0
CA B:HIS635 4.5 11.9 1.0
C B:SER633 4.5 15.4 1.0
CA B:LEU634 4.5 15.0 1.0
N B:HIS635 4.5 12.6 1.0
O B:HOH913 4.6 12.5 1.0
CG B:HIS635 4.6 15.9 1.0
C B:VAL613 4.6 16.3 1.0
OH B:TYR631 4.7 13.0 1.0
C B:HIS615 4.7 11.0 1.0
CA B:HIS614 4.7 11.0 1.0
N B:VAL613 4.7 11.3 1.0
CE1 B:HIS573 4.8 10.8 1.0
O B:TRP611 4.9 12.1 1.0
ND1 B:HIS573 4.9 12.2 1.0

Potassium binding site 4 out of 4 in 8d9a

Go back to Potassium Binding Sites List in 8d9a
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 8


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 Complexed with Fluorinated Inhibitor 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K804

b:16.2
occ:1.00
 O B:PHE623 2.7 15.7 1.0
O B:HOH948 2.7 20.0 1.0
O B:VAL629 2.7 14.9 1.0
O B:TYR662 2.7 16.4 1.0
O B:ASP626 2.9 22.4 1.0
O B:HOH938 3.1 15.2 1.0
C B:TYR662 3.6 20.5 1.0
C B:PHE623 3.6 13.3 1.0
CB B:TYR662 3.7 19.4 1.0
CB B:PHE623 3.7 14.3 1.0
C B:VAL629 3.9 17.1 1.0
C B:ASP626 4.0 18.8 1.0
CA B:TYR662 4.2 18.5 1.0
CA B:PHE623 4.3 15.1 1.0
N B:TYR631 4.4 12.6 1.0
N B:ASN663 4.4 21.3 1.0
N B:ASP626 4.4 18.7 1.0
CB B:ASP626 4.5 18.3 1.0
CA B:ASP626 4.5 17.7 1.0
N B:GLU624 4.5 15.9 1.0
CA B:LEU630 4.5 15.6 1.0
O B:GLU624 4.6 18.9 1.0
CA B:GLU624 4.7 18.8 1.0
C B:GLU624 4.7 18.3 1.0
N B:LEU630 4.7 15.0 1.0
CA B:ASN663 4.7 20.0 1.0
CB B:TYR631 4.7 14.2 1.0
CB B:ASN663 4.8 18.1 1.0
C B:LEU630 4.9 14.5 1.0
O B:GLY659 4.9 20.4 1.0
CG B:PHE623 5.0 14.4 1.0
CG B:TYR662 5.0 18.6 1.0
CA B:VAL629 5.0 14.1 1.0

Reference:

P.R.Watson, P.Bai, C.Wang, A.D.Cragin, J.M.Hooker, D.W.Christianson. Aromatic Ring Fluorination Patterns Modulate Inhibitory Potency of Fluorophenylhydroxamates Complexed with Histone Deacetylase 6. Biochemistry V. 61 1945 2022.
ISSN: ISSN 0006-2960
PubMed: 36073962
DOI: 10.1021/ACS.BIOCHEM.2C00332
Page generated: Mon Aug 12 23:27:55 2024

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