Atomistry » Potassium » PDB 8cxz-8eh1 » 8d9c
Atomistry »
  Potassium »
    PDB 8cxz-8eh1 »
      8d9c »

Potassium in PDB 8d9c: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 10

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 10, PDB code: 8d9c 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) 66.61 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.023, 92.02, 96.545, 90, 90, 90
R / Rfree (%) 17.8 / 21.5

Other elements in 8d9c:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 10 also contains other interesting chemical elements:

Fluorine (F) 10 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 Fluorinated Inhibitor 10 (pdb code 8d9c). 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 10, PDB code: 8d9c:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8d9c

Go back to Potassium Binding Sites List in 8d9c
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 10


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

b:13.7
occ:1.00
 O A:ASP612 2.6 13.1 1.0
O A:LEU634 2.6 15.8 1.0
OD1 A:ASP610 2.7 11.2 1.0
O A:HIS614 2.7 14.0 1.0
OG A:SER633 2.8 14.8 1.0
O A:ASP610 2.8 12.3 1.0
CG A:ASP610 3.2 16.2 1.0
C A:ASP610 3.5 14.9 1.0
C A:ASP612 3.6 14.0 1.0
C A:LEU634 3.7 14.9 1.0
C A:HIS614 3.7 14.8 1.0
CB A:ASP610 3.8 13.6 1.0
N A:ASP612 3.9 10.8 1.0
OD2 A:ASP610 3.9 16.0 1.0
CB A:SER633 3.9 12.3 1.0
N A:LEU634 3.9 13.3 1.0
CB A:HIS635 4.0 13.7 1.0
CA A:ASP612 4.1 10.0 1.0
C A:TRP611 4.2 12.9 1.0
N A:TRP611 4.2 12.8 1.0
CA A:ASP610 4.2 12.4 1.0
CB A:ASP612 4.3 13.6 1.0
CA A:HIS615 4.3 16.7 1.0
CA A:SER633 4.3 14.6 1.0
CA A:TRP611 4.3 13.9 1.0
N A:HIS615 4.3 16.1 1.0
N A:HIS614 4.4 13.5 1.0
ND1 A:HIS635 4.4 16.6 1.0
N A:GLY616 4.5 13.6 1.0
CA A:HIS635 4.5 12.8 1.0
CA A:LEU634 4.5 14.4 1.0
C A:SER633 4.5 16.8 1.0
N A:HIS635 4.5 12.6 1.0
O A:HOH919 4.6 12.9 1.0
CG A:HIS635 4.6 17.2 1.0
C A:VAL613 4.7 15.3 1.0
CA A:HIS614 4.7 12.6 1.0
N A:VAL613 4.7 10.6 1.0
C A:HIS615 4.7 13.5 1.0
OH A:TYR631 4.7 13.1 1.0
CE1 A:HIS573 4.8 13.1 1.0
O A:TRP611 4.9 12.1 1.0
ND1 A:HIS573 4.9 13.2 1.0

Potassium binding site 2 out of 4 in 8d9c

Go back to Potassium Binding Sites List in 8d9c
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 10


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

b:17.3
occ:1.00
 O A:PHE623 2.7 15.3 1.0
O A:HOH967 2.7 15.7 1.0
O A:VAL629 2.7 16.0 1.0
O A:TYR662 2.8 16.7 1.0
O A:ASP626 2.9 19.9 1.0
O A:HOH969 3.1 15.3 1.0
C A:TYR662 3.6 19.4 1.0
C A:PHE623 3.6 13.8 1.0
CB A:TYR662 3.7 19.2 1.0
CB A:PHE623 3.7 12.9 1.0
C A:VAL629 4.0 17.7 1.0
C A:ASP626 4.0 19.0 1.0
CA A:TYR662 4.3 17.2 1.0
CA A:PHE623 4.3 13.8 1.0
N A:TYR631 4.4 13.6 1.0
N A:ASP626 4.4 16.9 1.0
N A:ASN663 4.4 16.8 1.0
CB A:ASP626 4.5 15.3 1.0
CA A:ASP626 4.5 18.4 1.0
N A:GLU624 4.5 12.7 1.0
CA A:LEU630 4.6 15.3 1.0
CA A:GLU624 4.6 17.3 1.0
O A:GLU624 4.6 17.0 1.0
C A:GLU624 4.7 18.4 1.0
CB A:ASN663 4.7 16.8 1.0
CA A:ASN663 4.7 17.6 1.0
N A:LEU630 4.7 15.6 1.0
CB A:TYR631 4.7 12.2 1.0
O A:GLY659 4.9 19.1 1.0
C A:LEU630 4.9 15.5 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 8d9c

Go back to Potassium Binding Sites List in 8d9c
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 10


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

b:13.3
occ:1.00
 O B:ASP612 2.6 14.6 1.0
O B:LEU634 2.7 12.8 1.0
O B:HIS614 2.7 14.1 1.0
OD1 B:ASP610 2.7 11.8 1.0
OG B:SER633 2.8 12.4 1.0
O B:ASP610 2.8 12.8 1.0
CG B:ASP610 3.3 15.0 1.0
C B:ASP610 3.5 13.6 1.0
C B:ASP612 3.6 14.4 1.0
C B:HIS614 3.7 13.6 1.0
C B:LEU634 3.7 14.7 1.0
CB B:ASP610 3.8 14.6 1.0
N B:ASP612 3.9 10.6 1.0
N B:LEU634 3.9 12.3 1.0
CB B:SER633 4.0 10.3 1.0
OD2 B:ASP610 4.0 15.5 1.0
CB B:HIS635 4.0 16.1 1.0
CA B:ASP612 4.1 12.9 1.0
C B:TRP611 4.2 14.3 1.0
N B:TRP611 4.2 12.2 1.0
CA B:HIS615 4.2 13.2 1.0
CA B:ASP610 4.3 13.7 1.0
CB B:ASP612 4.3 12.9 1.0
CA B:SER633 4.3 12.4 1.0
N B:HIS615 4.3 13.9 1.0
CA B:TRP611 4.3 12.3 1.0
N B:HIS614 4.4 13.0 1.0
ND1 B:HIS635 4.4 15.3 1.0
N B:GLY616 4.4 14.5 1.0
C B:SER633 4.5 16.9 1.0
CA B:HIS635 4.5 14.4 1.0
CA B:LEU634 4.5 13.9 1.0
N B:HIS635 4.5 12.1 1.0
O B:HOH915 4.6 16.7 1.0
CG B:HIS635 4.7 17.1 1.0
C B:VAL613 4.7 12.6 1.0
CA B:HIS614 4.7 13.6 1.0
C B:HIS615 4.7 13.7 1.0
OH B:TYR631 4.7 10.8 1.0
N B:VAL613 4.7 11.4 1.0
O B:TRP611 4.9 14.5 1.0
CE1 B:HIS573 4.9 12.7 1.0
ND1 B:HIS573 4.9 12.6 1.0

Potassium binding site 4 out of 4 in 8d9c

Go back to Potassium Binding Sites List in 8d9c
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Fluorinated Inhibitor 10


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

b:15.6
occ:1.00
 O B:VAL629 2.7 14.1 1.0
O B:PHE623 2.7 14.4 1.0
O B:HOH955 2.8 14.5 1.0
O B:TYR662 2.8 14.9 1.0
O B:ASP626 2.9 18.4 1.0
O B:HOH1012 3.1 15.8 1.0
C B:TYR662 3.6 16.0 1.0
C B:PHE623 3.6 13.8 1.0
CB B:TYR662 3.7 17.4 1.0
CB B:PHE623 3.7 13.8 1.0
C B:VAL629 3.9 14.1 1.0
C B:ASP626 4.0 16.5 1.0
CA B:TYR662 4.3 17.6 1.0
CA B:PHE623 4.3 14.6 1.0
N B:TYR631 4.3 12.2 1.0
N B:ASP626 4.4 17.4 1.0
N B:ASN663 4.4 13.8 1.0
CA B:LEU630 4.5 12.7 1.0
N B:GLU624 4.6 14.8 1.0
CB B:ASP626 4.6 18.7 1.0
CA B:ASP626 4.6 17.6 1.0
CA B:GLU624 4.7 15.1 0.5
N B:LEU630 4.7 14.2 1.0
O B:GLU624 4.7 14.7 1.0
CA B:GLU624 4.7 15.1 0.5
CB B:TYR631 4.7 12.6 1.0
C B:GLU624 4.7 16.4 1.0
CB B:ASN663 4.7 13.3 1.0
CA B:ASN663 4.8 13.7 1.0
C B:LEU630 4.9 14.3 1.0
O B:GLY659 4.9 17.2 1.0
CA B:VAL629 5.0 13.1 1.0
CG B:PHE623 5.0 11.6 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 23:30:01 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy