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Potassium in PDB 5ef8: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat, PDB code: 5ef8 was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.71 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.168, 140.396, 91.856, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.4

Other elements in 5ef8:

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

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 in Complex with Panobinostat (pdb code 5ef8). 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 in Complex with Panobinostat, PDB code: 5ef8:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5ef8

Go back to Potassium Binding Sites List in 5ef8
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat


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 Panobinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2002

b:24.7
occ:1.00
 O A:ASP612 2.7 22.6 1.0
OD1 A:ASP610 2.8 26.6 1.0
O A:HIS614 2.8 20.9 1.0
OG A:SER633 2.8 16.9 1.0
O A:ASP610 2.8 21.5 1.0
O A:LEU634 2.9 21.8 1.0
CG A:ASP610 3.1 17.8 1.0
C A:ASP610 3.4 20.4 1.0
CB A:ASP610 3.6 18.4 1.0
C A:ASP612 3.7 21.8 1.0
C A:LEU634 3.7 19.8 1.0
C A:HIS614 3.8 22.9 1.0
N A:ASP612 3.8 20.6 1.0
OD2 A:ASP610 3.9 19.4 1.0
CB A:SER633 3.9 18.5 1.0
N A:LEU634 3.9 18.9 1.0
CB A:HIS635 4.0 19.1 1.0
CA A:ASP610 4.1 20.4 1.0
N A:TRP611 4.1 19.5 1.0
CA A:ASP612 4.2 21.4 1.0
CA A:HIS615 4.2 20.7 1.0
C A:TRP611 4.3 20.1 1.0
CA A:SER633 4.3 20.1 1.0
CB A:ASP612 4.3 21.6 1.0
CA A:TRP611 4.3 19.0 1.0
C A:SER633 4.3 19.8 1.0
N A:GLY616 4.4 21.3 1.0
N A:HIS615 4.4 22.3 1.0
N A:HIS635 4.5 19.3 1.0
CA A:LEU634 4.5 18.1 1.0
CA A:HIS635 4.5 20.2 1.0
ND1 A:HIS635 4.5 18.7 1.0
O A:HOH2110 4.6 12.9 1.0
N A:HIS614 4.6 20.9 1.0
CG A:HIS635 4.7 18.6 1.0
C A:HIS615 4.7 21.9 1.0
OH A:TYR631 4.8 18.7 1.0
N A:VAL613 4.8 20.6 1.0
C A:VAL613 4.8 22.4 1.0
CA A:HIS614 4.9 23.3 1.0

Potassium binding site 2 out of 4 in 5ef8

Go back to Potassium Binding Sites List in 5ef8
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat


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 Panobinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2003

b:28.9
occ:1.00
 O A:PHE623 2.7 31.5 1.0
O A:TYR662 2.8 27.3 1.0
O A:VAL629 2.8 28.2 1.0
O A:HOH2122 2.9 35.7 1.0
O A:ASP626 3.0 34.7 1.0
O A:HOH2116 3.2 26.7 1.0
C A:TYR662 3.5 27.3 1.0
CB A:TYR662 3.6 27.7 1.0
C A:PHE623 3.6 29.1 1.0
CB A:PHE623 3.8 27.4 1.0
C A:VAL629 4.0 29.5 1.0
C A:ASP626 4.2 34.0 1.0
CA A:TYR662 4.2 28.3 1.0
N A:TYR631 4.2 23.7 1.0
N A:ASN663 4.3 24.8 1.0
CA A:PHE623 4.4 27.1 1.0
CA A:LEU630 4.5 26.2 1.0
N A:GLU624 4.5 28.3 1.0
CB A:TYR631 4.6 21.9 1.0
N A:ASP626 4.6 32.9 1.0
CA A:GLU624 4.6 28.7 1.0
CB A:ASN663 4.6 24.9 1.0
CA A:ASN663 4.6 24.1 1.0
N A:LEU630 4.7 29.1 1.0
CA A:ASP626 4.7 33.2 1.0
C A:LEU630 4.8 25.2 1.0
C A:GLU624 4.8 32.0 1.0
O A:GLY659 4.8 31.4 1.0
CB A:ASP626 4.8 30.8 1.0
O A:GLU624 4.9 32.7 1.0
CG A:TYR662 4.9 31.6 1.0
OD1 A:ASN663 5.0 23.0 1.0

Potassium binding site 3 out of 4 in 5ef8

Go back to Potassium Binding Sites List in 5ef8
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat


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 Panobinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2002

b:22.6
occ:1.00
 O B:ASP612 2.7 15.2 1.0
O B:ASP610 2.8 17.4 1.0
OD1 B:ASP610 2.8 19.3 1.0
O B:HIS614 2.8 20.2 1.0
OG B:SER633 2.9 16.6 1.0
O B:LEU634 2.9 20.7 1.0
CG B:ASP610 3.1 17.9 1.0
CB B:ASP610 3.4 16.9 1.0
C B:ASP610 3.4 16.3 1.0
C B:ASP612 3.6 21.0 1.0
N B:ASP612 3.7 17.6 1.0
OD2 B:ASP610 3.7 18.1 1.0
C B:HIS614 3.8 20.4 1.0
C B:LEU634 3.8 17.7 1.0
CB B:SER633 4.0 17.2 1.0
CA B:ASP610 4.0 16.1 1.0
N B:LEU634 4.0 15.4 1.0
CA B:ASP612 4.0 19.1 1.0
CB B:ASP612 4.1 20.6 1.0
CB B:HIS635 4.1 19.2 1.0
CA B:HIS615 4.2 18.6 1.0
N B:TRP611 4.2 16.8 1.0
N B:GLY616 4.2 17.9 1.0
C B:TRP611 4.3 19.1 1.0
N B:HIS615 4.4 20.2 1.0
CA B:SER633 4.4 16.7 1.0
CA B:TRP611 4.5 17.9 1.0
ND1 B:HIS635 4.5 17.7 1.0
C B:SER633 4.5 16.6 1.0
C B:HIS615 4.6 18.9 1.0
CA B:LEU634 4.6 17.5 1.0
N B:HIS614 4.6 22.8 1.0
CA B:HIS635 4.6 18.9 1.0
N B:HIS635 4.6 17.2 1.0
OH B:TYR631 4.6 13.6 1.0
O B:HOH2115 4.8 19.2 1.0
N B:VAL613 4.8 17.9 1.0
CG B:HIS635 4.8 18.2 1.0
ND1 B:HIS573 4.8 19.4 1.0
C B:VAL613 4.8 21.5 1.0
CA B:HIS614 4.8 19.4 1.0
CE1 B:HIS573 4.9 20.5 1.0

Potassium binding site 4 out of 4 in 5ef8

Go back to Potassium Binding Sites List in 5ef8
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Panobinostat


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 Panobinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2003

b:21.2
occ:1.00
 O B:PHE623 2.6 22.3 1.0
O B:VAL629 2.8 19.0 1.0
O B:TYR662 2.8 19.6 1.0
O B:HOH2109 2.8 19.4 1.0
O B:ASP626 2.9 23.9 1.0
O B:HOH2124 3.1 18.9 1.0
C B:PHE623 3.6 22.1 1.0
C B:TYR662 3.6 20.6 1.0
CB B:TYR662 3.6 21.1 1.0
CB B:PHE623 3.7 20.5 1.0
C B:ASP626 4.0 24.3 1.0
C B:VAL629 4.0 20.0 1.0
CA B:TYR662 4.3 21.6 1.0
N B:TYR631 4.3 17.9 1.0
CA B:PHE623 4.3 20.7 1.0
N B:ASP626 4.5 25.9 1.0
N B:ASN663 4.5 20.6 1.0
N B:GLU624 4.5 23.1 1.0
CA B:ASP626 4.6 25.2 1.0
CB B:ASP626 4.6 21.9 1.0
CA B:LEU630 4.6 18.3 1.0
CB B:TYR631 4.6 18.0 1.0
CA B:GLU624 4.7 24.1 1.0
N B:LEU630 4.8 20.2 1.0
O B:GLY659 4.8 25.6 1.0
C B:GLU624 4.8 24.6 1.0
O B:GLU624 4.8 24.0 1.0
CA B:ASN663 4.8 19.9 1.0
CB B:ASN663 4.8 17.7 1.0
C B:LEU630 4.9 18.3 1.0
CG B:TYR662 4.9 23.5 1.0
CG B:PHE623 4.9 20.4 1.0
CA B:VAL629 5.0 20.7 1.0

Reference:

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134
Page generated: Mon Aug 12 13:26:29 2024

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