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Potassium in PDB 8d98: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5, PDB code: 8d98 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) 59.28 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.923, 91.468, 96.92, 90, 90, 90
R / Rfree (%) 18.3 / 21.1

Other elements in 8d98:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Fluorine (F) 4 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 5 (pdb code 8d98). 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 5, PDB code: 8d98:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8d98

Go back to Potassium Binding Sites List in 8d98
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5


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

b:14.6
occ:1.00
 O A:ASP612 2.6 15.1 1.0
O A:LEU634 2.7 15.1 1.0
O A:HIS614 2.7 15.6 1.0
OG A:SER633 2.8 14.6 1.0
OD1 A:ASP610 2.8 12.4 1.0
O A:ASP610 2.9 14.0 1.0
CG A:ASP610 3.3 14.0 1.0
C A:ASP610 3.5 14.1 1.0
C A:ASP612 3.6 14.5 1.0
C A:HIS614 3.7 12.9 1.0
C A:LEU634 3.7 15.1 1.0
N A:ASP612 3.8 13.2 1.0
CB A:ASP610 3.8 13.2 1.0
OD2 A:ASP610 3.9 16.3 1.0
CB A:SER633 3.9 12.7 1.0
CB A:HIS635 4.0 15.1 1.0
N A:LEU634 4.0 13.4 1.0
CA A:ASP612 4.1 12.2 1.0
CB A:ASP612 4.2 14.7 1.0
C A:TRP611 4.2 14.4 1.0
N A:TRP611 4.2 12.5 1.0
CA A:HIS615 4.3 12.9 1.0
CA A:ASP610 4.3 12.6 1.0
CA A:TRP611 4.3 15.7 1.0
ND1 A:HIS635 4.3 16.0 1.0
N A:HIS615 4.4 11.8 1.0
CA A:SER633 4.4 13.9 1.0
N A:HIS614 4.4 13.3 1.0
N A:GLY616 4.5 13.4 1.0
CA A:HIS635 4.5 13.8 1.0
CA A:LEU634 4.5 15.8 1.0
C A:SER633 4.5 17.2 1.0
N A:HIS635 4.6 14.6 1.0
O A:HOH910 4.6 16.7 1.0
CG A:HIS635 4.6 14.6 1.0
C A:VAL613 4.7 14.7 1.0
N A:VAL613 4.7 13.6 1.0
CA A:HIS614 4.7 14.8 1.0
C A:HIS615 4.7 12.1 1.0
OH A:TYR631 4.8 13.6 1.0
CE1 A:HIS573 4.8 15.4 1.0
O A:TRP611 4.9 13.2 1.0
ND1 A:HIS573 5.0 14.9 1.0

Potassium binding site 2 out of 4 in 8d98

Go back to Potassium Binding Sites List in 8d98
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K804

b:16.5
occ:1.00
 O A:HOH950 2.6 17.5 1.0
O A:PHE623 2.7 15.8 1.0
O A:VAL629 2.7 15.2 1.0
O A:TYR662 2.7 16.5 1.0
O A:ASP626 2.9 20.1 1.0
O A:HOH948 3.0 15.8 1.0
C A:TYR662 3.6 16.9 1.0
C A:PHE623 3.7 16.0 1.0
CB A:TYR662 3.7 16.9 1.0
CB A:PHE623 3.7 16.0 1.0
C A:VAL629 3.9 17.4 1.0
C A:ASP626 4.1 19.8 1.0
CA A:TYR662 4.3 15.9 1.0
CA A:PHE623 4.3 16.4 1.0
N A:TYR631 4.3 12.3 1.0
N A:ASN663 4.4 17.1 1.0
N A:ASP626 4.5 17.4 1.0
N A:GLU624 4.6 15.0 1.0
CA A:LEU630 4.6 13.4 1.0
CA A:GLU624 4.6 14.4 1.0
CB A:ASP626 4.6 13.6 1.0
CA A:ASP626 4.6 16.0 1.0
O A:GLU624 4.7 16.6 1.0
C A:GLU624 4.7 17.9 1.0
N A:LEU630 4.7 13.4 1.0
CA A:ASN663 4.7 13.6 1.0
CB A:ASN663 4.8 14.7 1.0
CB A:TYR631 4.8 13.0 1.0
C A:LEU630 4.9 13.7 1.0
O A:GLY659 5.0 19.4 1.0
CG A:PHE623 5.0 13.6 1.0
CA A:VAL629 5.0 13.8 1.0

Potassium binding site 3 out of 4 in 8d98

Go back to Potassium Binding Sites List in 8d98
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5


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

b:12.7
occ:1.00
 O B:ASP612 2.6 13.9 1.0
O B:LEU634 2.7 12.4 1.0
O B:HIS614 2.7 12.5 1.0
OD1 B:ASP610 2.7 13.7 1.0
OG B:SER633 2.8 14.1 1.0
O B:ASP610 2.8 12.3 1.0
CG B:ASP610 3.2 13.4 1.0
C B:ASP610 3.5 13.5 1.0
C B:ASP612 3.6 14.5 1.0
C B:HIS614 3.7 12.9 1.0
C B:LEU634 3.7 12.0 1.0
CB B:ASP610 3.8 12.6 1.0
N B:ASP612 3.9 12.5 1.0
OD2 B:ASP610 3.9 14.4 1.0
N B:LEU634 4.0 12.2 1.0
CB B:HIS635 4.0 12.3 1.0
CB B:SER633 4.0 11.0 1.0
CA B:ASP612 4.1 12.9 1.0
CB B:ASP612 4.2 13.3 1.0
C B:TRP611 4.2 12.7 1.0
CA B:HIS615 4.2 11.5 1.0
N B:TRP611 4.3 12.2 1.0
CA B:ASP610 4.3 14.0 1.0
N B:HIS615 4.3 12.5 1.0
ND1 B:HIS635 4.3 12.3 1.0
CA B:SER633 4.4 10.7 1.0
CA B:TRP611 4.4 12.1 1.0
N B:HIS614 4.4 11.7 1.0
O B:HOH931 4.5 15.3 1.0
CA B:HIS635 4.5 12.3 1.0
N B:GLY616 4.5 12.8 1.0
CA B:LEU634 4.5 11.9 1.0
C B:SER633 4.5 12.8 1.0
N B:HIS635 4.5 12.2 1.0
CG B:HIS635 4.6 10.3 1.0
C B:VAL613 4.7 14.7 1.0
CA B:HIS614 4.7 10.1 1.0
C B:HIS615 4.7 10.5 1.0
N B:VAL613 4.7 9.2 1.0
OH B:TYR631 4.7 13.1 1.0
CE1 B:HIS573 4.9 15.0 1.0
O B:TRP611 4.9 11.4 1.0
ND1 B:HIS573 5.0 15.3 1.0

Potassium binding site 4 out of 4 in 8d98

Go back to Potassium Binding Sites List in 8d98
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K804

b:13.5
occ:1.00
 O B:VAL629 2.7 14.8 1.0
O B:PHE623 2.7 14.6 1.0
O B:HOH930 2.7 12.8 1.0
O B:TYR662 2.8 12.7 1.0
O B:ASP626 2.9 16.8 1.0
O B:HOH962 3.0 13.7 1.0
C B:TYR662 3.6 11.7 1.0
C B:PHE623 3.7 13.2 1.0
CB B:TYR662 3.7 13.0 1.0
CB B:PHE623 3.7 13.4 1.0
C B:VAL629 3.9 12.8 1.0
C B:ASP626 4.1 15.8 1.0
CA B:TYR662 4.3 14.3 1.0
N B:TYR631 4.3 10.5 1.0
CA B:PHE623 4.3 11.0 1.0
N B:ASN663 4.4 11.6 1.0
N B:ASP626 4.5 14.9 1.0
CA B:LEU630 4.6 12.4 1.0
N B:GLU624 4.6 13.3 1.0
CA B:GLU624 4.6 13.1 1.0
CA B:ASP626 4.6 11.7 1.0
CB B:ASP626 4.7 15.4 1.0
N B:LEU630 4.7 12.4 1.0
O B:GLU624 4.7 15.4 1.0
C B:GLU624 4.7 14.8 1.0
CB B:TYR631 4.7 10.7 1.0
CA B:ASN663 4.8 11.7 1.0
CB B:ASN663 4.8 11.5 1.0
O B:GLY659 4.9 14.6 1.0
C B:LEU630 4.9 11.3 1.0
CA B:VAL629 5.0 14.0 1.0
OD1 B:ASN663 5.0 14.0 1.0
CG B:PHE623 5.0 14.4 1.0
CG B:TYR662 5.0 14.7 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 23:27:48 2024

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