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Potassium in PDB 7o2p: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756, PDB code: 7o2p was solved by K.Zrubek, G.Sandrone, C.D.Cukier, A.Stevenazzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.42 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.483, 90.753, 71.964, 90, 95.64, 90
R / Rfree (%) 19.5 / 26.1

Other elements in 7o2p:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756 also contains other interesting chemical elements:

Iodine (I) 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 ITF3756 (pdb code 7o2p). 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 ITF3756, PDB code: 7o2p:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 7o2p

Go back to Potassium Binding Sites List in 7o2p
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756


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 ITF3756 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:28.1
occ:1.00
 O A:PHE623 2.5 29.2 1.0
O A:HOH940 2.5 26.4 1.0
O A:TYR662 2.6 28.9 1.0
O A:VAL629 2.7 27.8 1.0
O A:HOH954 2.9 24.9 1.0
O A:ASP626 3.0 36.4 1.0
C A:TYR662 3.5 27.2 1.0
C A:PHE623 3.5 25.4 1.0
CB A:TYR662 3.7 30.8 1.0
CB A:PHE623 3.7 28.5 1.0
C A:VAL629 3.9 25.0 1.0
C A:ASP626 4.1 34.6 1.0
CA A:TYR662 4.2 28.9 1.0
N A:ASN663 4.2 28.6 1.0
CA A:PHE623 4.2 28.8 1.0
N A:GLU624 4.4 25.1 1.0
N A:TYR631 4.4 25.8 1.0
CA A:GLU624 4.5 27.4 1.0
N A:ASP626 4.6 35.3 1.0
C A:GLU624 4.6 28.9 1.0
CA A:ASN663 4.6 27.2 1.0
CB A:ASN663 4.6 28.0 1.0
CA A:LEU630 4.7 24.2 1.0
O A:GLU624 4.7 28.2 1.0
CB A:TYR631 4.7 22.6 1.0
N A:LEU630 4.7 26.4 1.0
CA A:ASP626 4.7 32.3 1.0
CB A:ASP626 4.8 33.3 1.0
O A:GLY659 4.8 32.7 1.0
CA A:VAL629 4.9 27.4 1.0
C A:LEU630 4.9 24.6 1.0
CB A:VAL629 5.0 27.8 1.0

Potassium binding site 2 out of 4 in 7o2p

Go back to Potassium Binding Sites List in 7o2p
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756


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 ITF3756 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K804

b:27.4
occ:1.00
 O A:ASP612 2.4 19.7 1.0
O A:HIS614 2.6 18.1 1.0
OG A:SER633 2.7 24.6 1.0
O A:LEU634 2.7 20.4 1.0
OD1 A:ASP610 2.8 23.8 1.0
O A:ASP610 2.8 21.0 1.0
CG A:ASP610 3.3 25.5 1.0
C A:ASP610 3.5 20.3 1.0
C A:HIS614 3.6 19.1 1.0
C A:ASP612 3.6 21.6 1.0
C A:LEU634 3.7 21.0 1.0
CB A:ASP610 3.8 25.1 1.0
CB A:HIS635 3.9 20.9 1.0
N A:ASP612 3.9 20.8 1.0
CB A:SER633 3.9 25.3 1.0
N A:LEU634 4.0 21.4 1.0
OD2 A:ASP610 4.1 25.8 1.0
CA A:ASP612 4.1 20.4 1.0
N A:HIS615 4.2 19.9 1.0
CB A:ASP612 4.2 20.9 1.0
C A:TRP611 4.2 21.1 1.0
N A:TRP611 4.2 20.0 1.0
CA A:ASP610 4.2 23.3 1.0
CA A:HIS615 4.2 21.4 1.0
ND1 A:HIS635 4.3 22.3 1.0
CA A:SER633 4.3 26.4 1.0
N A:HIS614 4.3 20.2 1.0
CA A:TRP611 4.4 19.8 1.0
CA A:HIS635 4.4 19.6 1.0
N A:HIS635 4.5 19.8 1.0
O A:HOH906 4.5 19.1 1.0
C A:SER633 4.5 24.7 1.0
CG A:HIS635 4.5 20.1 1.0
CA A:LEU634 4.5 22.5 1.0
C A:VAL613 4.5 18.9 1.0
N A:GLY616 4.6 22.3 1.0
CA A:HIS614 4.6 19.8 1.0
N A:VAL613 4.6 18.1 1.0
CE1 A:HIS573 4.7 28.1 1.0
C A:HIS615 4.8 21.5 1.0
OH A:TYR631 4.8 23.5 1.0
O A:TRP611 4.9 22.2 1.0
ND1 A:HIS573 4.9 25.2 1.0
O A:VAL613 4.9 20.2 1.0
CA A:VAL613 5.0 19.6 1.0

Potassium binding site 3 out of 4 in 7o2p

Go back to Potassium Binding Sites List in 7o2p
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756


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 ITF3756 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:34.1
occ:1.00
 O B:HOH920 2.5 28.6 1.0
O B:TYR662 2.6 27.5 1.0
O B:PHE623 2.6 34.7 1.0
O B:VAL629 2.7 30.9 1.0
O B:HOH963 2.9 25.5 1.0
O B:ASP626 3.0 43.3 1.0
C B:PHE623 3.5 34.7 1.0
C B:TYR662 3.5 29.6 1.0
CB B:PHE623 3.7 30.4 1.0
CB B:TYR662 3.7 32.3 1.0
C B:VAL629 3.9 30.0 1.0
C B:ASP626 4.2 44.4 1.0
CA B:PHE623 4.2 32.5 1.0
CA B:TYR662 4.2 31.2 1.0
N B:TYR631 4.3 28.5 1.0
N B:GLU624 4.4 34.8 1.0
N B:ASN663 4.4 32.4 1.0
CA B:LEU630 4.5 28.1 1.0
CA B:GLU624 4.5 33.0 1.0
N B:ASP626 4.5 38.8 1.0
N B:LEU630 4.6 28.8 1.0
CB B:ASP626 4.7 43.4 1.0
CA B:ASP626 4.7 40.3 1.0
O B:GLY659 4.7 41.9 1.0
C B:GLU624 4.7 32.7 1.0
CB B:ASN663 4.8 31.6 1.0
CA B:ASN663 4.8 30.6 1.0
C B:LEU630 4.8 27.6 1.0
CB B:TYR631 4.8 26.1 1.0
O B:GLU624 4.9 27.4 1.0
CA B:VAL629 4.9 32.4 1.0
CG B:PHE623 5.0 30.0 1.0

Potassium binding site 4 out of 4 in 7o2p

Go back to Potassium Binding Sites List in 7o2p
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with ITF3756


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 ITF3756 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K804

b:27.3
occ:1.00
 O B:ASP612 2.4 16.5 1.0
O B:LEU634 2.6 16.7 1.0
OG B:SER633 2.7 21.6 1.0
O B:HIS614 2.7 17.3 1.0
OD1 B:ASP610 2.7 18.3 1.0
O B:ASP610 2.8 19.9 1.0
CG B:ASP610 3.3 20.9 1.0
C B:ASP610 3.4 20.0 1.0
C B:ASP612 3.5 20.4 1.0
C B:LEU634 3.6 18.4 1.0
C B:HIS614 3.7 19.3 1.0
N B:ASP612 3.8 20.3 1.0
CB B:ASP610 3.9 21.8 1.0
CB B:SER633 3.9 24.1 1.0
N B:LEU634 3.9 19.4 1.0
CB B:HIS635 4.0 19.9 1.0
OD2 B:ASP610 4.0 23.4 1.0
N B:TRP611 4.0 19.0 1.0
CA B:ASP612 4.0 20.0 1.0
C B:TRP611 4.2 19.9 1.0
CB B:ASP612 4.2 19.6 1.0
CA B:ASP610 4.2 19.5 1.0
CA B:TRP611 4.3 19.9 1.0
CA B:SER633 4.3 22.8 1.0
O B:HOH940 4.3 19.1 1.0
ND1 B:HIS635 4.4 22.2 1.0
N B:HIS614 4.4 20.5 1.0
N B:HIS635 4.4 19.4 1.0
CA B:HIS635 4.4 20.9 1.0
N B:HIS615 4.4 20.8 1.0
CA B:HIS615 4.4 21.3 1.0
CA B:LEU634 4.5 19.3 1.0
C B:SER633 4.5 20.4 1.0
N B:VAL613 4.6 19.4 1.0
N B:GLY616 4.6 23.6 1.0
CG B:HIS635 4.6 21.9 1.0
C B:VAL613 4.6 19.3 1.0
CA B:HIS614 4.7 18.3 1.0
OH B:TYR631 4.7 23.3 1.0
CE1 B:HIS573 4.7 20.1 1.0
ND1 B:HIS573 4.9 17.3 1.0
O B:TRP611 4.9 19.4 1.0
C B:HIS615 4.9 23.1 1.0
CA B:VAL613 5.0 19.2 1.0

Reference:

G.Sandrone, C.D.Cukier, K.Zrubek, M.Marchini, B.Vergani, G.Caprini, G.Fossati, C.Steinkuhler, A.Stevenazzi. Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00425
Page generated: Mon Aug 12 19:36:08 2024

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