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Potassium in PDB 8g1z: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ317

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ317, PDB code: 8g1z was solved by M.A.Tararina, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.57 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.657, 48.39, 74.521, 90, 106.18, 90
R / Rfree (%) 20.5 / 25.5

Other elements in 8g1z:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ317 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ317 (pdb code 8g1z). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ317, PDB code: 8g1z:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 8g1z

Go back to Potassium Binding Sites List in 8g1z
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ317


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 Complexed with Inhibitor MZ317 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:20.9
occ:1.00
O A:ASP612 2.6 17.4 1.0
O A:LEU634 2.7 20.4 1.0
OD1 A:ASP610 2.7 23.2 1.0
O A:HIS614 2.7 23.1 1.0
OG A:SER633 2.8 22.5 1.0
O A:ASP610 2.8 16.9 1.0
CG A:ASP610 3.2 23.3 1.0
C A:ASP610 3.5 22.4 1.0
C A:ASP612 3.6 19.7 1.0
C A:LEU634 3.7 18.9 1.0
C A:HIS614 3.7 24.8 1.0
CB A:ASP610 3.7 22.7 1.0
N A:ASP612 3.8 20.8 1.0
N A:LEU634 3.9 16.9 1.0
OD2 A:ASP610 3.9 19.8 1.0
CB A:SER633 3.9 19.4 1.0
CB A:HIS635 4.1 17.8 1.0
CA A:ASP612 4.1 25.7 1.0
CB A:ASP612 4.2 22.9 1.0
CA A:ASP610 4.2 21.0 1.0
N A:TRP611 4.2 19.0 1.0
C A:TRP611 4.2 23.5 1.0
CA A:SER633 4.3 19.5 1.0
CA A:HIS615 4.3 18.8 1.0
CA A:TRP611 4.4 23.0 1.0
N A:HIS615 4.4 22.6 1.0
ND1 A:HIS635 4.4 20.0 1.0
CA A:LEU634 4.4 20.4 1.0
C A:SER633 4.4 25.1 1.0
N A:HIS614 4.5 19.5 1.0
N A:GLY616 4.5 19.3 1.0
CA A:HIS635 4.5 21.8 1.0
N A:HIS635 4.5 21.1 1.0
OH A:TYR631 4.7 18.3 1.0
O A:HOH928 4.7 20.9 1.0
C A:VAL613 4.7 19.8 1.0
N A:VAL613 4.7 20.3 1.0
CA A:HIS614 4.7 20.6 1.0
CG A:HIS635 4.7 18.4 1.0
C A:HIS615 4.8 19.8 1.0
CE1 A:HIS573 4.9 22.2 1.0
OD1 A:ASP612 5.0 21.8 1.0
ND1 A:HIS573 5.0 18.6 1.0

Potassium binding site 2 out of 2 in 8g1z

Go back to Potassium Binding Sites List in 8g1z
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ317


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 Complexed with Inhibitor MZ317 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K804

b:21.9
occ:1.00
O A:VAL629 2.7 22.4 1.0
O A:PHE623 2.7 23.2 1.0
O A:TYR662 2.7 22.0 1.0
O A:HOH941 2.8 19.2 1.0
O A:ASP626 2.9 24.7 1.0
O A:HOH1011 2.9 21.9 1.0
C A:TYR662 3.6 20.7 1.0
CB A:TYR662 3.6 24.3 1.0
C A:PHE623 3.7 24.9 1.0
CB A:PHE623 3.7 19.7 1.0
C A:VAL629 3.9 22.9 1.0
C A:ASP626 4.1 25.9 1.0
CA A:TYR662 4.2 20.7 1.0
CA A:PHE623 4.3 21.8 1.0
N A:TYR631 4.4 19.2 1.0
N A:ASN663 4.5 19.2 1.0
N A:ASP626 4.5 20.9 1.0
CA A:LEU630 4.5 19.9 1.0
N A:GLU624 4.6 24.0 1.0
N A:LEU630 4.7 21.2 1.0
O A:GLU624 4.7 21.7 1.0
CA A:ASP626 4.7 26.2 1.0
CA A:GLU624 4.7 26.1 1.0
CB A:ASP626 4.7 23.5 1.0
C A:GLU624 4.7 22.9 1.0
CB A:ASN663 4.8 18.3 1.0
CA A:ASN663 4.8 19.5 1.0
CB A:TYR631 4.8 20.1 1.0
C A:LEU630 4.9 22.7 1.0
O A:GLY659 4.9 20.8 1.0
CA A:VAL629 4.9 21.1 1.0
CG A:TYR662 4.9 25.0 1.0
CG A:PHE623 5.0 20.1 1.0

Reference:

L.Sinatra, A.Vogelmann, F.Friedrich, M.A.Tararina, E.Neuwirt, A.Colcerasa, P.Konig, L.Toy, T.Z.Yesiloglu, S.Hilscher, L.Gaitzsch, N.Papenkordt, S.Zhai, L.Zhang, C.Romier, O.Einsle, W.Sippl, M.Schutkowski, O.Gross, G.Bendas, D.W.Christianson, F.K.Hansen, M.Jung, M.Schiedel. Development of First-in-Class Dual SIRT2/HDAC6 Inhibitors As Molecular Tools For Dual Inhibition of Tubulin Deacetylation. J.Med.Chem. V. 66 14787 2023.
ISSN: ISSN 0022-2623
PubMed: 37902787
DOI: 10.1021/ACS.JMEDCHEM.3C01385
Page generated: Sat Aug 9 16:54:07 2025

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