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Potassium in PDB 6vnr: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor, PDB code: 6vnr was solved by J.D.Osko, 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) 48.38 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.380, 107.140, 74.350, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.1

Other elements in 6vnr:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor 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 (CD2) Complexed with Bishydroxamic Acid Inhibitor (pdb code 6vnr). 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 (CD2) Complexed with Bishydroxamic Acid Inhibitor, PDB code: 6vnr:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6vnr

Go back to Potassium Binding Sites List in 6vnr
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid 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 (CD2) Complexed with Bishydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:7.5
occ:1.00
 O A:ASP612 2.5 5.0 1.0
O A:LEU634 2.7 6.3 1.0
O A:HIS614 2.7 6.3 1.0
OD1 A:ASP610 2.8 4.0 1.0
O A:ASP610 2.9 6.5 1.0
OG A:SER633 2.9 6.0 1.0
CG A:ASP610 3.2 5.0 1.0
C A:ASP610 3.5 7.5 1.0
C A:ASP612 3.6 5.2 1.0
C A:LEU634 3.7 8.9 1.0
C A:HIS614 3.7 5.6 1.0
N A:ASP612 3.8 4.9 1.0
OD2 A:ASP610 3.8 6.8 1.0
CB A:ASP610 3.8 3.7 1.0
CB A:HIS635 3.9 3.6 1.0
N A:LEU634 3.9 5.1 1.0
CB A:SER633 4.0 6.0 1.0
CA A:ASP612 4.1 5.6 1.0
N A:TRP611 4.2 4.5 1.0
C A:TRP611 4.2 6.7 1.0
CB A:ASP612 4.2 4.6 1.0
CA A:ASP610 4.3 4.5 1.0
CA A:HIS615 4.3 5.2 1.0
ND1 A:HIS635 4.3 6.8 1.0
CA A:TRP611 4.3 7.6 1.0
N A:HIS615 4.3 7.2 1.0
CA A:SER633 4.4 5.5 1.0
N A:HIS614 4.4 4.7 1.0
CA A:LEU634 4.5 4.2 1.0
CA A:HIS635 4.5 9.8 1.0
N A:GLY616 4.5 4.5 1.0
C A:SER633 4.5 5.2 1.0
N A:HIS635 4.5 5.5 1.0
CG A:HIS635 4.6 7.9 1.0
O A:HOH934 4.6 6.8 1.0
C A:VAL613 4.7 7.1 1.0
CA A:HIS614 4.7 5.9 1.0
N A:VAL613 4.7 7.1 1.0
OH A:TYR631 4.7 6.0 1.0
C A:HIS615 4.7 8.7 1.0
CE1 A:HIS573 4.8 7.9 1.0
ND1 A:HIS573 5.0 6.9 1.0
O A:TRP611 5.0 5.5 1.0

Potassium binding site 2 out of 4 in 6vnr

Go back to Potassium Binding Sites List in 6vnr
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid 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 (CD2) Complexed with Bishydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:6.9
occ:1.00
 O A:VAL629 2.6 6.6 1.0
O A:PHE623 2.7 6.5 1.0
O A:HOH942 2.7 5.2 1.0
O A:TYR662 2.8 4.3 1.0
O A:ASP626 2.9 13.8 1.0
O A:HOH1056 3.0 6.8 1.0
C A:TYR662 3.6 6.1 1.0
CB A:TYR662 3.6 4.2 1.0
C A:PHE623 3.7 6.0 1.0
CB A:PHE623 3.8 5.4 1.0
C A:VAL629 3.9 4.5 1.0
C A:ASP626 4.1 11.4 1.0
CA A:TYR662 4.2 4.7 1.0
N A:TYR631 4.3 2.8 1.0
CA A:PHE623 4.4 6.4 1.0
N A:ASN663 4.4 3.0 1.0
N A:ASP626 4.5 5.9 1.0
CA A:LEU630 4.5 3.4 1.0
N A:GLU624 4.6 4.0 1.0
CA A:GLU624 4.6 6.4 1.0
CA A:ASP626 4.6 10.8 1.0
N A:LEU630 4.6 5.7 1.0
CB A:ASP626 4.7 9.8 1.0
O A:GLU624 4.7 8.3 1.0
C A:GLU624 4.7 7.8 1.0
CB A:TYR631 4.8 2.4 1.0
CA A:ASN663 4.8 4.0 1.0
CB A:ASN663 4.8 4.3 1.0
C A:LEU630 4.8 6.2 1.0
CG A:TYR662 4.9 8.8 1.0
CA A:VAL629 4.9 5.8 1.0
O A:GLY659 4.9 7.8 1.0

Potassium binding site 3 out of 4 in 6vnr

Go back to Potassium Binding Sites List in 6vnr
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid 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 (CD2) Complexed with Bishydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:5.4
occ:1.00
 O B:ASP612 2.6 5.4 1.0
O B:LEU634 2.7 5.4 1.0
O B:HIS614 2.7 9.7 1.0
OD1 B:ASP610 2.8 3.1 1.0
OG B:SER633 2.8 5.4 1.0
O B:ASP610 2.9 9.0 1.0
CG B:ASP610 3.2 7.1 1.0
C B:ASP610 3.5 6.0 1.0
C B:ASP612 3.6 6.5 1.0
C B:HIS614 3.7 7.2 1.0
C B:LEU634 3.7 5.7 1.0
CB B:ASP610 3.7 4.3 1.0
OD2 B:ASP610 3.8 5.5 1.0
N B:ASP612 3.9 6.3 1.0
CB B:HIS635 3.9 3.4 1.0
CB B:SER633 4.0 8.4 1.0
N B:LEU634 4.0 3.9 1.0
CA B:ASP612 4.1 7.2 1.0
N B:TRP611 4.2 3.4 1.0
CA B:ASP610 4.2 4.2 1.0
C B:TRP611 4.2 4.6 1.0
CB B:ASP612 4.3 5.6 1.0
CA B:HIS615 4.3 5.8 1.0
CA B:SER633 4.3 7.5 1.0
CA B:TRP611 4.3 4.2 1.0
ND1 B:HIS635 4.3 5.4 1.0
N B:HIS615 4.4 9.3 1.0
N B:GLY616 4.4 6.0 1.0
N B:HIS614 4.4 5.3 1.0
CA B:HIS635 4.5 5.5 1.0
C B:SER633 4.5 5.2 1.0
CA B:LEU634 4.5 4.6 1.0
N B:HIS635 4.6 5.5 1.0
O B:HOH972 4.6 6.6 1.0
CG B:HIS635 4.6 5.7 1.0
OH B:TYR631 4.6 6.2 1.0
C B:VAL613 4.7 9.8 1.0
C B:HIS615 4.7 6.2 1.0
CA B:HIS614 4.7 4.8 1.0
N B:VAL613 4.7 7.5 1.0
CE1 B:HIS573 4.8 5.9 1.0
ND1 B:HIS573 4.9 7.3 1.0
O B:TRP611 5.0 6.0 1.0

Potassium binding site 4 out of 4 in 6vnr

Go back to Potassium Binding Sites List in 6vnr
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid 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 (CD2) Complexed with Bishydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:7.9
occ:1.00
 O B:PHE623 2.6 3.2 1.0
O B:HOH951 2.7 8.0 1.0
O B:VAL629 2.7 6.7 1.0
O B:TYR662 2.8 7.2 1.0
O B:ASP626 2.9 7.1 1.0
O B:HOH964 3.1 5.8 1.0
C B:TYR662 3.5 8.6 1.0
CB B:TYR662 3.6 2.6 1.0
C B:PHE623 3.6 4.6 1.0
CB B:PHE623 3.7 3.7 1.0
C B:VAL629 3.9 6.2 1.0
C B:ASP626 4.1 7.7 1.0
CA B:TYR662 4.2 5.1 1.0
CA B:PHE623 4.3 2.7 1.0
N B:ASN663 4.4 5.0 1.0
N B:TYR631 4.4 1.9 1.0
N B:ASP626 4.5 6.6 1.0
N B:GLU624 4.5 4.4 1.0
CA B:GLU624 4.6 5.2 1.0
CA B:LEU630 4.6 5.0 1.0
CA B:ASP626 4.6 6.3 1.0
C B:GLU624 4.7 6.6 1.0
CB B:ASP626 4.7 7.1 0.8
N B:LEU630 4.7 6.1 1.0
O B:GLU624 4.7 6.5 1.0
CA B:ASN663 4.7 6.2 1.0
O B:GLY659 4.8 4.5 1.0
CB B:ASN663 4.8 5.8 1.0
CB B:TYR631 4.8 7.4 1.0
CG B:TYR662 4.9 7.0 1.0
C B:LEU630 4.9 6.4 1.0
CA B:VAL629 5.0 5.3 1.0
CG B:PHE623 5.0 3.4 1.0

Reference:

A.K.Miller, M.Morgen, R.R.Steimbach, M.Geraldy, L.Hellweg, P.Sehr, J.Ridinger, O.Witt, I.Oehme, C.J.Herbst-Gervasoni, J.D.Osko, N.J.Porter, D.W.Christianson, N.Gunkel. Design and Synthesis of Dihydroxamic Acids As HDAC6/8/10 Inhibitors. Chemmedchem 2020.
ISSN: ESSN 1860-7187
PubMed: 32348628
DOI: 10.1002/CMDC.202000149
Page generated: Mon Aug 12 18:01:07 2024

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