Potassium in PDB 8a8z: Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924

Protein crystallography data

The structure of Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924, PDB code: 8a8z 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) 47.88 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.372, 118.924, 60.263, 90, 93.87, 90
R / Rfree (%) 15.5 / 19

Other elements in 8a8z:

The structure of Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 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 HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 (pdb code 8a8z). 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 HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924, PDB code: 8a8z:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8a8z

Go back to Potassium Binding Sites List in 8a8z
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924


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 HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:19.1
occ:1.00
 O A:VAL629 2.6 18.0 1.0
O A:PHE623 2.7 17.3 1.0
O A:HOH1043 2.7 17.3 1.0
O A:TYR662 2.8 17.2 1.0
O A:ASP626 2.9 22.3 1.0
O A:HOH1030 3.0 18.6 1.0
C A:TYR662 3.6 16.9 1.0
C A:PHE623 3.6 15.6 1.0
CB A:TYR662 3.7 18.8 1.0
CB A:PHE623 3.7 16.6 1.0
C A:VAL629 3.8 17.0 1.0
C A:ASP626 4.1 25.0 1.0
CA A:TYR662 4.2 17.5 1.0
CA A:PHE623 4.3 16.3 1.0
N A:ASN663 4.4 15.6 1.0
N A:TYR631 4.4 15.6 1.0
N A:ASP626 4.5 23.3 1.0
CA A:LEU630 4.5 15.4 1.0
N A:GLU624 4.6 18.9 1.0
N A:LEU630 4.6 16.3 1.0
CA A:ASP626 4.7 23.9 1.0
CA A:GLU624 4.7 20.2 1.0
O A:GLU624 4.7 21.6 1.0
CA A:ASN663 4.8 15.8 1.0
CB A:ASP626 4.8 27.8 1.0
C A:GLU624 4.8 20.9 1.0
CB A:TYR631 4.8 14.9 1.0
CB A:ASN663 4.8 15.9 1.0
CA A:VAL629 4.9 17.0 1.0
C A:LEU630 4.9 15.3 1.0
O A:GLY659 4.9 20.1 1.0
CG A:PHE623 5.0 17.4 1.0

Potassium binding site 2 out of 4 in 8a8z

Go back to Potassium Binding Sites List in 8a8z
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924


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 HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K804

b:15.5
occ:1.00
 O A:ASP612 2.5 14.2 1.0
O A:LEU634 2.6 16.5 1.0
O A:HIS614 2.7 15.0 1.0
OD1 A:ASP610 2.7 16.2 1.0
OG A:SER633 2.8 15.3 1.0
O A:ASP610 2.8 15.1 1.0
CG A:ASP610 3.3 16.8 1.0
C A:ASP610 3.5 15.8 1.0
C A:ASP612 3.6 16.4 1.0
C A:HIS614 3.7 16.0 1.0
C A:LEU634 3.7 16.8 1.0
CB A:ASP610 3.9 16.2 1.0
N A:ASP612 3.9 16.5 1.0
CB A:SER633 3.9 15.2 1.0
N A:LEU634 3.9 15.6 1.0
OD2 A:ASP610 4.0 18.4 1.0
CB A:HIS635 4.1 14.7 1.0
CA A:ASP612 4.1 15.9 1.0
N A:TRP611 4.2 15.1 1.0
CA A:ASP610 4.2 16.5 1.0
C A:TRP611 4.2 16.1 1.0
CB A:ASP612 4.3 16.4 1.0
CA A:SER633 4.3 15.6 1.0
CA A:HIS615 4.3 15.3 1.0
N A:HIS615 4.3 15.7 1.0
CA A:TRP611 4.4 15.1 1.0
ND1 A:HIS635 4.4 16.6 1.0
N A:HIS614 4.5 13.7 1.0
C A:SER633 4.5 17.0 1.0
N A:GLY616 4.5 16.9 1.0
O A:HOH937 4.5 20.0 1.0
CA A:LEU634 4.5 15.8 1.0
N A:HIS635 4.6 15.6 1.0
CA A:HIS635 4.6 15.7 1.0
N A:VAL613 4.7 14.9 1.0
CG A:HIS635 4.7 15.3 1.0
CE1 A:HIS573 4.7 17.3 1.0
OH A:TYR631 4.7 18.8 1.0
CA A:HIS614 4.7 15.1 1.0
C A:VAL613 4.7 13.8 1.0
C A:HIS615 4.8 15.7 1.0
ND1 A:HIS573 4.8 16.8 1.0
O A:TRP611 4.9 16.6 1.0

Potassium binding site 3 out of 4 in 8a8z

Go back to Potassium Binding Sites List in 8a8z
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924


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 HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:17.1
occ:1.00
 O B:ASP612 2.6 14.8 1.0
O B:LEU634 2.7 16.5 1.0
OD1 B:ASP610 2.7 17.1 1.0
OG B:SER633 2.7 16.1 1.0
O B:ASP610 2.8 15.2 1.0
O B:HIS614 2.8 15.9 1.0
CG B:ASP610 3.3 18.7 1.0
C B:ASP610 3.5 16.4 1.0
C B:ASP612 3.6 16.4 1.0
C B:LEU634 3.7 17.7 1.0
C B:HIS614 3.7 16.9 1.0
CB B:SER633 3.9 16.1 1.0
CB B:ASP610 3.9 17.3 1.0
N B:ASP612 3.9 16.3 1.0
N B:LEU634 3.9 16.4 1.0
OD2 B:ASP610 3.9 20.5 1.0
CB B:HIS635 4.0 16.6 1.0
N B:TRP611 4.1 15.1 1.0
CA B:ASP612 4.1 15.9 1.0
CA B:SER633 4.2 16.3 1.0
C B:TRP611 4.2 15.2 1.0
CA B:ASP610 4.3 15.5 1.0
CB B:ASP612 4.3 15.9 1.0
CA B:HIS615 4.3 17.0 1.0
CA B:TRP611 4.4 14.2 1.0
ND1 B:HIS635 4.4 17.4 1.0
N B:HIS615 4.4 15.7 1.0
C B:SER633 4.4 17.2 1.0
N B:HIS614 4.5 16.7 1.0
O B:HOH954 4.5 19.8 1.0
N B:GLY616 4.5 17.8 1.0
CA B:HIS635 4.5 16.3 1.0
CA B:LEU634 4.5 17.5 1.0
N B:HIS635 4.6 17.0 1.0
CE1 B:HIS573 4.7 19.8 1.0
C B:VAL613 4.7 17.2 1.0
CG B:HIS635 4.7 17.6 1.0
N B:VAL613 4.7 16.2 1.0
OH B:TYR631 4.7 17.3 1.0
CA B:HIS614 4.8 17.1 1.0
C B:HIS615 4.8 17.1 1.0
ND1 B:HIS573 4.9 18.3 1.0
O B:TRP611 4.9 16.7 1.0

Potassium binding site 4 out of 4 in 8a8z

Go back to Potassium Binding Sites List in 8a8z
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924


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 HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K804

b:19.8
occ:1.00
 O B:VAL629 2.6 17.0 1.0
O B:HOH1020 2.6 18.6 1.0
O B:PHE623 2.7 20.0 1.0
O B:TYR662 2.8 16.5 1.0
O B:ASP626 2.9 24.0 1.0
O B:HOH1026 3.0 18.2 1.0
C B:TYR662 3.6 18.2 1.0
C B:PHE623 3.6 18.1 1.0
CB B:TYR662 3.7 17.8 1.0
CB B:PHE623 3.7 19.9 1.0
C B:VAL629 3.8 17.0 1.0
C B:ASP626 4.0 23.3 1.0
CA B:TYR662 4.2 18.4 1.0
CA B:PHE623 4.3 19.0 1.0
N B:TYR631 4.3 15.0 1.0
N B:ASN663 4.4 17.2 1.0
N B:ASP626 4.4 24.6 1.0
N B:GLU624 4.5 21.2 1.0
CA B:LEU630 4.6 16.5 1.0
CA B:ASP626 4.6 23.6 1.0
O B:GLU624 4.7 21.0 1.0
N B:LEU630 4.7 16.6 1.0
CA B:GLU624 4.7 22.6 1.0
C B:GLU624 4.7 21.4 1.0
CB B:ASP626 4.7 27.3 1.0
CA B:ASN663 4.8 15.6 1.0
CB B:ASN663 4.9 15.6 1.0
O B:GLY659 4.9 21.4 1.0
CB B:TYR631 4.9 14.7 1.0
CA B:VAL629 4.9 17.4 1.0
C B:LEU630 4.9 16.2 1.0
CG B:TYR662 5.0 19.2 1.0

Reference:

E.Cellupica, G.Caprini, P.Cordella, C.Cukier, G.Fossati, M.Marchini, I.Rocchio, G.Sandrone, M.A.Vanoni, B.Vergani, K.Zrubek, A.Stevenazzi, C.Steinkuhler. Difluoromethyl-1,3,4-Oxadiazoles Are Slow-Binding Substrate Analog Inhibitors of Histone Deacetylase 6 with Unprecedented Isotype Selectivity. J.Biol.Chem. V. 299 02800 2022.
ISSN: ESSN 1083-351X
PubMed: 36528061
DOI: 10.1016/J.JBC.2022.102800
Page generated: Wed Apr 5 10:34:54 2023

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