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Potassium in PDB 5eem: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2

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

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2, PDB code: 5eem 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) 15.91 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.485, 55.400, 74.183, 73.58, 89.84, 82.64
R / Rfree (%) 22.4 / 27.3

Other elements in 5eem:

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

Zinc (Zn) 2 atoms
Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (pdb code 5eem). 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, PDB code: 5eem:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5eem

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:13.6
occ:1.00
 O B:PHE623 2.7 13.1 1.0
O B:HOH943 2.7 15.0 1.0
O B:VAL629 2.7 12.7 1.0
O B:ASP626 2.9 22.4 1.0
O B:TYR662 2.9 14.2 1.0
O B:HOH999 3.0 14.6 1.0
C B:PHE623 3.6 15.5 1.0
C B:TYR662 3.6 15.7 1.0
CB B:TYR662 3.7 16.2 1.0
CB B:PHE623 3.8 13.1 1.0
C B:VAL629 4.0 13.0 1.0
C B:ASP626 4.0 22.1 1.0
CA B:TYR662 4.3 15.3 1.0
CA B:PHE623 4.3 13.8 1.0
N B:TYR631 4.4 13.7 1.0
N B:ASN663 4.4 11.2 1.0
N B:ASP626 4.4 21.6 1.0
N B:GLU624 4.5 15.7 1.0
CA B:GLU624 4.5 19.5 1.0
CB B:ASP626 4.5 21.9 1.0
CA B:ASP626 4.5 21.9 1.0
O B:GLU624 4.6 20.2 1.0
C B:GLU624 4.7 19.8 1.0
CA B:LEU630 4.7 12.3 1.0
O B:GLY659 4.7 16.5 1.0
CA B:ASN663 4.8 13.3 1.0
N B:LEU630 4.8 14.3 1.0
CB B:ASN663 4.8 12.9 1.0
CB B:TYR631 4.8 13.9 1.0
CA B:VAL629 4.9 13.6 1.0
CG B:PHE623 5.0 12.3 1.0

Potassium binding site 2 out of 4 in 5eem

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


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

b:15.3
occ:1.00
 O B:LEU634 2.6 12.4 1.0
O B:ASP610 2.6 9.1 1.0
O B:ASP612 2.6 10.4 1.0
OG B:SER633 2.7 12.4 1.0
OD1 B:ASP610 2.7 10.7 1.0
O B:HIS614 2.8 12.6 1.0
CG B:ASP610 3.2 10.2 1.0
C B:ASP610 3.3 8.6 1.0
C B:LEU634 3.6 12.1 1.0
CB B:ASP610 3.6 10.0 1.0
C B:ASP612 3.7 12.1 1.0
C B:HIS614 3.8 11.3 1.0
N B:LEU634 3.8 11.4 1.0
N B:ASP612 3.8 9.5 1.0
CB B:SER633 3.9 11.4 1.0
CB B:HIS635 3.9 10.5 1.0
OD2 B:ASP610 4.0 11.2 1.0
N B:TRP611 4.1 8.1 1.0
CA B:ASP610 4.1 9.7 1.0
CA B:ASP612 4.1 9.5 1.0
C B:TRP611 4.2 8.2 1.0
CB B:ASP612 4.3 8.5 1.0
CA B:TRP611 4.3 8.9 1.0
CA B:SER633 4.3 11.2 1.0
CA B:HIS615 4.3 12.1 1.0
CA B:LEU634 4.4 11.6 1.0
N B:HIS615 4.4 11.5 1.0
C B:SER633 4.4 12.8 1.0
CA B:HIS635 4.4 11.2 1.0
N B:HIS635 4.4 10.6 1.0
O B:HOH953 4.4 7.7 1.0
ND1 B:HIS635 4.5 9.6 1.0
N B:GLY616 4.5 12.2 1.0
N B:HIS614 4.6 8.9 1.0
CG B:HIS635 4.7 10.9 1.0
OH B:TYR631 4.7 12.7 1.0
N B:VAL613 4.8 11.8 1.0
C B:VAL613 4.8 10.0 1.0
C B:HIS615 4.8 11.8 1.0
CA B:HIS614 4.8 10.1 1.0

Potassium binding site 3 out of 4 in 5eem

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:14.4
occ:1.00
 O A:LEU634 2.6 12.1 1.0
O A:ASP612 2.7 12.8 1.0
O A:ASP610 2.7 7.8 1.0
OD1 A:ASP610 2.7 8.2 1.0
O A:HIS614 2.8 12.3 1.0
OG A:SER633 2.8 10.8 1.0
CG A:ASP610 3.2 9.7 1.0
C A:ASP610 3.4 7.8 1.0
C A:LEU634 3.6 11.2 1.0
C A:HIS614 3.7 13.2 1.0
CB A:ASP610 3.7 8.9 1.0
C A:ASP612 3.7 12.2 1.0
N A:LEU634 3.8 11.6 1.0
N A:ASP612 3.9 9.9 1.0
OD2 A:ASP610 3.9 8.8 1.0
CB A:SER633 3.9 8.4 1.0
CB A:HIS635 4.0 11.2 1.0
N A:TRP611 4.1 7.6 1.0
CA A:ASP610 4.1 8.3 1.0
CA A:HIS615 4.2 13.3 1.0
CA A:ASP612 4.2 11.7 1.0
C A:TRP611 4.3 10.1 1.0
CA A:SER633 4.3 10.9 1.0
N A:HIS615 4.3 12.0 1.0
CA A:TRP611 4.3 9.3 1.0
ND1 A:HIS635 4.3 11.1 1.0
CA A:LEU634 4.3 12.8 1.0
C A:SER633 4.3 13.6 1.0
CB A:ASP612 4.4 10.3 1.0
N A:HIS635 4.5 9.0 1.0
CA A:HIS635 4.5 10.5 1.0
N A:GLY616 4.5 9.9 1.0
N A:HIS614 4.6 8.1 1.0
CG A:HIS635 4.6 12.3 1.0
O A:HOH920 4.7 11.8 1.0
C A:HIS615 4.7 12.1 1.0
OH A:TYR631 4.7 13.1 1.0
CA A:HIS614 4.8 9.3 1.0
C A:VAL613 4.8 9.3 1.0
N A:VAL613 4.8 12.7 1.0

Potassium binding site 4 out of 4 in 5eem

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


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

b:13.7
occ:1.00
 O A:PHE623 2.6 14.3 1.0
O A:HOH931 2.7 9.0 1.0
O A:VAL629 2.7 9.8 1.0
O A:TYR662 2.8 10.9 1.0
O A:ASP626 2.9 17.8 1.0
O A:HOH992 2.9 14.6 1.0
C A:PHE623 3.6 14.9 1.0
C A:TYR662 3.6 12.3 1.0
CB A:TYR662 3.7 13.8 1.0
CB A:PHE623 3.7 12.3 1.0
C A:ASP626 4.0 18.2 1.0
C A:VAL629 4.0 12.6 1.0
CA A:TYR662 4.3 12.2 1.0
CA A:PHE623 4.3 14.3 1.0
N A:TYR631 4.3 11.2 1.0
N A:ASP626 4.4 18.4 1.0
N A:ASN663 4.4 9.8 1.0
N A:GLU624 4.5 15.3 1.0
CB A:ASP626 4.5 20.8 1.0
CA A:ASP626 4.5 19.1 1.0
CA A:GLU624 4.6 18.6 1.0
CA A:LEU630 4.6 11.6 1.0
O A:GLU624 4.7 16.9 1.0
C A:GLU624 4.7 18.4 1.0
CA A:ASN663 4.7 10.7 1.0
CB A:ASN663 4.7 10.7 1.0
CB A:TYR631 4.8 9.5 1.0
O A:GLY659 4.8 16.8 1.0
N A:LEU630 4.8 13.1 1.0
CG A:PHE623 5.0 11.9 1.0
C A:LEU630 5.0 12.3 1.0
CA A:VAL629 5.0 12.9 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 13:24:47 2024

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