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Potassium in PDB 6mr5: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor, PDB code: 6mr5 was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.010, 46.460, 96.400, 90.00, 119.19, 90.00
R / Rfree (%) 19 / 22.6

Other elements in 6mr5:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 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 in Complex with A Mercaptoacetamide-Based Inhibitor (pdb code 6mr5). 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 A Mercaptoacetamide-Based Inhibitor, PDB code: 6mr5:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6mr5

Go back to Potassium Binding Sites List in 6mr5
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:17.2
occ:1.00
O A:ASP612 2.7 22.9 1.0
O A:LEU634 2.7 19.0 1.0
O A:HIS614 2.8 22.0 1.0
O A:ASP610 2.8 19.6 1.0
OG A:SER633 2.8 20.1 1.0
OD1 A:ASP610 2.9 17.9 1.0
CG A:ASP610 3.2 16.2 1.0
C A:ASP610 3.5 18.6 1.0
C A:ASP612 3.7 18.6 1.0
C A:HIS614 3.7 23.4 1.0
C A:LEU634 3.7 21.6 1.0
CB A:ASP610 3.7 19.1 1.0
OD2 A:ASP610 3.9 19.8 1.0
N A:ASP612 3.9 16.4 1.0
CB A:SER633 3.9 20.2 1.0
N A:LEU634 4.0 15.8 1.0
CB A:HIS635 4.0 21.1 1.0
CA A:HIS615 4.1 21.9 1.0
CA A:ASP612 4.1 18.6 1.0
CA A:ASP610 4.2 16.9 1.0
CB A:ASP612 4.2 18.3 1.0
N A:TRP611 4.3 16.3 1.0
N A:HIS615 4.3 21.9 1.0
CA A:SER633 4.3 21.1 1.0
C A:TRP611 4.3 17.2 1.0
N A:GLY616 4.3 20.0 1.0
ND1 A:HIS635 4.4 21.5 1.0
CA A:TRP611 4.4 16.6 1.0
C A:SER633 4.4 20.8 1.0
CA A:HIS635 4.5 25.5 1.0
N A:HIS614 4.5 25.6 1.0
N A:HIS635 4.5 21.9 1.0
CA A:LEU634 4.5 21.4 1.0
C A:HIS615 4.6 23.6 1.0
O A:HOH916 4.6 23.2 1.0
CG A:HIS635 4.6 25.2 1.0
OH A:TYR631 4.6 17.7 1.0
C A:VAL613 4.7 21.8 1.0
CA A:HIS614 4.7 23.1 1.0
N A:VAL613 4.8 19.4 1.0
CE1 A:HIS573 4.9 19.8 1.0
ND1 A:HIS573 4.9 20.5 1.0

Potassium binding site 2 out of 4 in 6mr5

Go back to Potassium Binding Sites List in 6mr5
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:23.3
occ:1.00
O A:VAL629 2.7 20.8 1.0
O A:HOH952 2.7 19.8 1.0
O A:PHE623 2.7 21.9 1.0
O A:TYR662 2.8 19.6 1.0
O A:ASP626 2.9 24.9 1.0
O A:HOH973 3.0 24.3 1.0
C A:TYR662 3.6 23.3 1.0
CB A:TYR662 3.6 20.3 1.0
C A:PHE623 3.7 21.7 1.0
CB A:PHE623 3.8 18.4 1.0
C A:VAL629 3.9 21.1 1.0
C A:ASP626 4.1 25.7 1.0
CA A:TYR662 4.2 20.8 1.0
N A:TYR631 4.4 21.5 1.0
N A:ASN663 4.4 18.4 1.0
CA A:PHE623 4.4 17.6 1.0
CA A:LEU630 4.5 19.7 1.0
CA A:GLU624 4.5 24.4 1.0
N A:ASP626 4.5 26.0 1.0
N A:GLU624 4.5 19.7 1.0
O A:GLU624 4.6 22.1 1.0
N A:LEU630 4.7 20.3 1.0
C A:GLU624 4.7 22.2 1.0
CA A:ASP626 4.7 22.4 1.0
CA A:ASN663 4.8 20.7 1.0
CB A:ASP626 4.8 26.9 1.0
CB A:ASN663 4.8 19.9 1.0
CB A:TYR631 4.8 17.5 1.0
O A:GLY659 4.9 23.3 1.0
C A:LEU630 4.9 19.0 1.0
CG A:TYR662 4.9 22.0 1.0
CA A:VAL629 5.0 21.6 1.0

Potassium binding site 3 out of 4 in 6mr5

Go back to Potassium Binding Sites List in 6mr5
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:16.9
occ:1.00
O B:ASP612 2.6 15.9 1.0
O B:LEU634 2.7 17.3 1.0
O B:HIS614 2.8 18.9 1.0
OD1 B:ASP610 2.8 16.3 1.0
O B:ASP610 2.8 16.5 1.0
OG B:SER633 2.8 13.9 1.0
CG B:ASP610 3.2 14.8 1.0
C B:ASP610 3.5 15.7 1.0
C B:ASP612 3.6 15.1 1.0
C B:LEU634 3.7 17.4 1.0
C B:HIS614 3.7 19.1 1.0
CB B:ASP610 3.7 12.5 1.0
N B:ASP612 3.8 13.5 1.0
OD2 B:ASP610 3.9 16.8 1.0
N B:LEU634 3.9 17.2 1.0
CB B:SER633 3.9 15.2 1.0
CB B:HIS635 4.0 15.6 1.0
CA B:ASP612 4.1 14.0 1.0
CA B:HIS615 4.2 19.7 1.0
CB B:ASP612 4.2 14.4 1.0
CA B:ASP610 4.2 14.6 1.0
N B:TRP611 4.2 13.1 1.0
C B:TRP611 4.2 13.8 1.0
CA B:SER633 4.3 17.6 1.0
N B:HIS615 4.3 17.6 1.0
ND1 B:HIS635 4.4 17.1 1.0
CA B:TRP611 4.4 13.3 1.0
C B:SER633 4.4 16.6 1.0
CA B:HIS635 4.4 14.8 1.0
N B:GLY616 4.5 16.5 1.0
CA B:LEU634 4.5 18.9 1.0
N B:HIS614 4.5 16.4 1.0
N B:HIS635 4.5 14.4 1.0
O B:HOH974 4.5 17.9 1.0
CG B:HIS635 4.6 17.4 1.0
OH B:TYR631 4.7 15.9 1.0
C B:HIS615 4.7 16.6 1.0
C B:VAL613 4.7 16.6 1.0
CA B:HIS614 4.7 19.0 1.0
N B:VAL613 4.8 15.2 1.0
CE1 B:HIS573 4.8 17.8 1.0
ND1 B:HIS573 4.9 16.6 1.0

Potassium binding site 4 out of 4 in 6mr5

Go back to Potassium Binding Sites List in 6mr5
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:21.8
occ:1.00
O B:PHE623 2.6 19.3 1.0
O B:HOH931 2.7 18.5 1.0
O B:VAL629 2.7 18.8 1.0
O B:TYR662 2.8 17.2 1.0
O B:ASP626 2.9 21.1 1.0
O B:HOH1000 3.1 19.6 1.0
C B:TYR662 3.6 18.4 1.0
C B:PHE623 3.6 21.3 1.0
CB B:TYR662 3.6 21.5 1.0
CB B:PHE623 3.8 18.7 1.0
C B:VAL629 3.9 15.6 1.0
C B:ASP626 4.1 21.8 1.0
CA B:TYR662 4.2 19.7 1.0
N B:TYR631 4.3 15.8 1.0
CA B:PHE623 4.3 21.1 1.0
N B:ASN663 4.4 16.5 1.0
N B:ASP626 4.4 21.9 1.0
N B:GLU624 4.5 19.1 1.0
CA B:LEU630 4.5 16.8 1.0
CA B:GLU624 4.6 22.7 1.0
CA B:ASP626 4.6 20.5 1.0
CB B:ASP626 4.6 19.5 1.0
C B:GLU624 4.7 22.7 1.0
N B:LEU630 4.7 16.0 1.0
O B:GLU624 4.7 21.1 1.0
CB B:ASN663 4.7 17.3 1.0
CA B:ASN663 4.7 18.0 1.0
CB B:TYR631 4.8 18.9 1.0
O B:GLY659 4.8 19.8 1.0
C B:LEU630 4.9 19.0 1.0
CA B:VAL629 4.9 19.1 1.0
CG B:TYR662 4.9 20.6 1.0

Reference:

N.J.Porter, S.Shen, C.Barinka, A.P.Kozikowski, D.W.Christianson. Molecular Basis For the Selective Inhibition of Histone Deacetylase 6 By A Mercaptoacetamide Inhibitor. Acs Med Chem Lett V. 9 1301 2018.
ISSN: ISSN 1948-5875
PubMed: 30613344
DOI: 10.1021/ACSMEDCHEMLETT.8B00487
Page generated: Mon Dec 14 00:55:21 2020

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