Potassium in PDB 8gd4: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6, PDB code: 8gd4 was solved by P.R.Watson, A.D.Craigin, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.56 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.803, 92.364, 96.474, 90, 90, 90
R / Rfree (%) 18.5 / 22.2

Other elements in 8gd4:

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

Fluorine (F) 4 atoms
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 Complexed with Dmfo Inhibitor 6 (pdb code 8gd4). 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 Dmfo Inhibitor 6, PDB code: 8gd4:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8gd4

Go back to Potassium Binding Sites List in 8gd4
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6


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 Dmfo Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:11.3
occ:1.00
O A:LEU634 2.6 8.6 1.0
O A:ASP612 2.7 10.6 1.0
O A:HIS614 2.7 13.0 1.0
OG A:SER633 2.7 10.1 1.0
O A:ASP610 2.8 12.2 1.0
OD1 A:ASP610 2.8 11.5 1.0
CG A:ASP610 3.3 10.4 1.0
C A:ASP610 3.5 10.3 1.0
C A:LEU634 3.6 9.5 1.0
C A:HIS614 3.6 11.9 1.0
C A:ASP612 3.7 10.5 1.0
CB A:ASP610 3.9 5.4 1.0
CB A:SER633 3.9 10.1 1.0
N A:LEU634 3.9 10.4 1.0
CB A:HIS635 3.9 12.0 1.0
N A:ASP612 4.0 9.9 1.0
OD2 A:ASP610 4.0 9.9 1.0
CA A:HIS615 4.2 13.1 1.0
CA A:ASP612 4.2 7.8 1.0
CA A:SER633 4.2 11.3 1.0
N A:TRP611 4.3 9.2 1.0
N A:HIS615 4.3 11.2 1.0
C A:TRP611 4.3 11.0 1.0
CA A:ASP610 4.3 9.4 1.0
ND1 A:HIS635 4.3 11.4 1.0
CB A:ASP612 4.4 7.6 1.0
C A:SER633 4.4 12.7 1.0
CA A:TRP611 4.4 9.2 1.0
CA A:LEU634 4.4 11.6 0.2
CA A:LEU634 4.4 11.6 0.8
N A:HIS614 4.4 10.6 1.0
N A:GLY616 4.4 9.8 1.0
CA A:HIS635 4.5 8.4 1.0
N A:HIS635 4.5 10.1 1.0
CG A:HIS635 4.6 8.8 1.0
O A:HOH917 4.6 9.7 1.0
C A:HIS615 4.7 12.4 1.0
CA A:HIS614 4.7 9.9 1.0
OH A:TYR631 4.7 11.3 1.0
C A:VAL613 4.7 10.8 1.0
N A:VAL613 4.8 10.2 1.0
CE1 A:HIS573 4.8 9.6 1.0
ND1 A:HIS573 4.9 11.2 1.0

Potassium binding site 2 out of 4 in 8gd4

Go back to Potassium Binding Sites List in 8gd4
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6


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 Dmfo Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K804

b:12.6
occ:1.00
O A:PHE623 2.6 8.5 1.0
O A:VAL629 2.7 12.7 1.0
O A:HOH909 2.7 12.2 1.0
O A:TYR662 2.8 12.1 1.0
O A:ASP626 2.8 15.3 1.0
O A:HOH919 3.2 11.6 1.0
C A:PHE623 3.6 11.8 1.0
C A:TYR662 3.6 15.4 1.0
CB A:TYR662 3.7 15.7 1.0
CB A:PHE623 3.7 8.5 1.0
C A:ASP626 3.9 15.1 1.0
C A:VAL629 4.0 11.1 1.0
CA A:TYR662 4.3 13.5 1.0
CA A:PHE623 4.3 11.6 1.0
N A:TYR631 4.3 10.3 1.0
N A:ASP626 4.4 14.5 1.0
N A:ASN663 4.4 12.8 1.0
N A:GLU624 4.5 12.3 1.0
CA A:GLU624 4.5 12.4 1.0
CA A:ASP626 4.5 17.6 1.0
CA A:LEU630 4.6 9.2 1.0
CB A:ASP626 4.6 14.7 1.0
C A:GLU624 4.6 15.7 1.0
O A:GLU624 4.6 14.2 1.0
CB A:TYR631 4.7 9.8 1.0
N A:LEU630 4.7 12.0 1.0
CA A:ASN663 4.8 13.1 1.0
O A:GLY659 4.8 15.7 1.0
CB A:ASN663 4.8 13.1 1.0
C A:LEU630 4.9 13.7 1.0
CG A:PHE623 5.0 9.1 1.0
CA A:VAL629 5.0 12.7 1.0

Potassium binding site 3 out of 4 in 8gd4

Go back to Potassium Binding Sites List in 8gd4
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6


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 Dmfo Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:11.0
occ:1.00
O B:ASP612 2.6 11.7 1.0
O B:LEU634 2.6 9.0 1.0
O B:HIS614 2.7 10.7 1.0
OD1 B:ASP610 2.8 10.7 1.0
O B:ASP610 2.8 10.9 1.0
OG B:SER633 2.9 9.3 1.0
CG B:ASP610 3.3 9.6 1.0
C B:ASP610 3.5 10.5 1.0
C B:ASP612 3.6 11.4 1.0
C B:HIS614 3.7 10.5 1.0
C B:LEU634 3.7 11.7 1.0
CB B:ASP610 3.8 6.2 1.0
N B:ASP612 3.9 9.9 1.0
CB B:SER633 3.9 9.0 1.0
N B:LEU634 4.0 10.0 1.0
CB B:HIS635 4.0 12.9 1.0
OD2 B:ASP610 4.0 8.7 1.0
CA B:ASP612 4.1 8.7 1.0
N B:TRP611 4.2 8.9 1.0
CB B:ASP612 4.2 6.9 1.0
CA B:HIS615 4.2 10.8 1.0
C B:TRP611 4.2 10.3 1.0
CA B:ASP610 4.3 8.1 1.0
CA B:SER633 4.3 12.3 1.0
N B:HIS615 4.3 7.3 1.0
CA B:TRP611 4.4 11.8 1.0
ND1 B:HIS635 4.4 11.0 1.0
N B:HIS614 4.4 7.6 1.0
N B:GLY616 4.4 8.0 1.0
C B:SER633 4.5 11.1 1.0
CA B:HIS635 4.5 8.8 1.0
CA B:LEU634 4.5 12.2 1.0
N B:HIS635 4.5 10.1 1.0
O B:HOH909 4.6 8.8 1.0
C B:VAL613 4.6 9.0 1.0
CG B:HIS635 4.7 9.4 1.0
OH B:TYR631 4.7 9.7 1.0
CA B:HIS614 4.7 10.4 1.0
C B:HIS615 4.7 10.8 1.0
N B:VAL613 4.7 8.8 1.0
CE1 B:HIS573 4.7 14.2 1.0
ND1 B:HIS573 4.9 10.2 1.0
O B:TRP611 5.0 11.1 1.0
CA B:VAL613 5.0 10.8 1.0

Potassium binding site 4 out of 4 in 8gd4

Go back to Potassium Binding Sites List in 8gd4
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6


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 Dmfo Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K804

b:12.7
occ:1.00
O B:VAL629 2.6 11.5 1.0
O B:PHE623 2.7 12.9 1.0
O B:HOH959 2.8 12.0 1.0
O B:TYR662 2.8 11.5 1.0
O B:ASP626 2.9 14.8 1.0
O B:HOH991 3.1 9.8 1.0
C B:TYR662 3.6 17.2 1.0
CB B:TYR662 3.6 11.5 1.0
C B:PHE623 3.6 11.6 1.0
CB B:PHE623 3.8 11.6 1.0
C B:VAL629 3.9 10.3 1.0
C B:ASP626 4.0 14.2 1.0
CA B:TYR662 4.2 12.1 1.0
N B:TYR631 4.3 11.6 1.0
CA B:PHE623 4.4 12.7 1.0
N B:ASP626 4.4 16.4 1.0
N B:ASN663 4.4 12.8 1.0
CA B:LEU630 4.5 11.6 1.0
N B:GLU624 4.5 12.4 1.0
CA B:ASP626 4.6 17.6 1.0
CA B:GLU624 4.6 14.1 1.0
CB B:ASP626 4.6 16.4 1.0
N B:LEU630 4.6 8.5 1.0
C B:GLU624 4.7 14.4 1.0
O B:GLU624 4.7 10.9 1.0
CB B:TYR631 4.8 9.3 1.0
CA B:ASN663 4.8 11.1 1.0
O B:GLY659 4.8 18.7 1.0
CB B:ASN663 4.8 12.3 1.0
C B:LEU630 4.9 14.2 1.0
CA B:VAL629 4.9 13.9 1.0
CG B:TYR662 4.9 15.6 1.0

Reference:

B.Konig, P.R.Watson, N.Rebing, A.D.Craigin, L.Schaker-Hubner, D.W.Christianson, F.K.Hansen. Difluoromethyl-1,3,4-Oxadiazoles Are Selective, Mechanism-Based, and Essentially Irreversible Inhibitors of Histone Deacetylase 6 To Be Published.
Page generated: Mon Aug 12 23:49:52 2024

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