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Potassium in PDB 6q0z: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JS28

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JS28, PDB code: 6q0z was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.80 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.170, 55.340, 74.240, 73.04, 89.86, 83.01
R / Rfree (%) n/a / n/a

Other elements in 6q0z:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JS28 also contains other interesting chemical elements:

Bromine (Br) 2 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 Complexed with JS28 (pdb code 6q0z). 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 Complexed with JS28, PDB code: 6q0z:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6q0z

Go back to Potassium Binding Sites List in 6q0z
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JS28


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 JS28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:11.6
occ:1.00
 O A:ASP612 2.5 12.2 1.0
O A:HIS614 2.7 12.4 1.0
OG A:SER633 2.8 9.9 1.0
O A:LEU634 2.8 11.9 1.0
O A:ASP610 2.8 10.4 1.0
OD1 A:ASP610 2.9 11.8 1.0
CG A:ASP610 3.3 10.6 1.0
C A:ASP610 3.5 12.4 1.0
C A:ASP612 3.6 11.2 1.0
C A:HIS614 3.7 14.5 1.0
C A:LEU634 3.7 9.6 1.0
CB A:ASP610 3.8 11.9 1.0
CB A:SER633 3.8 8.0 1.0
N A:LEU634 3.9 13.6 1.0
N A:ASP612 3.9 8.3 1.0
OD2 A:ASP610 3.9 8.8 1.0
CB A:HIS635 4.0 8.6 1.0
CA A:ASP612 4.2 8.9 1.0
N A:TRP611 4.2 11.6 1.0
CA A:ASP610 4.2 11.9 1.0
ND1 A:HIS635 4.2 10.3 1.0
CB A:ASP612 4.3 8.9 1.0
C A:TRP611 4.3 10.3 1.0
CA A:SER633 4.3 8.9 1.0
CA A:HIS615 4.3 12.9 1.0
N A:HIS615 4.3 13.0 1.0
CA A:TRP611 4.4 12.6 1.0
N A:HIS614 4.4 7.9 1.0
CA A:HIS635 4.4 11.0 1.0
C A:SER633 4.5 9.5 1.0
N A:GLY616 4.5 12.5 1.0
CA A:LEU634 4.5 10.6 1.0
O A:HOH925 4.5 9.6 1.0
N A:HIS635 4.5 13.0 1.0
CG A:HIS635 4.6 12.3 1.0
C A:VAL613 4.6 12.7 1.0
OH A:TYR631 4.7 10.3 1.0
CA A:HIS614 4.7 11.0 1.0
N A:VAL613 4.7 9.7 1.0
C A:HIS615 4.8 13.6 1.0
CE1 A:HIS573 4.9 11.9 1.0
ND1 A:HIS573 5.0 12.1 1.0

Potassium binding site 2 out of 4 in 6q0z

Go back to Potassium Binding Sites List in 6q0z
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JS28


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 JS28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:15.1
occ:1.00
 O A:PHE623 2.6 13.3 1.0
O A:VAL629 2.7 13.4 1.0
O A:HOH909 2.8 13.5 1.0
O A:TYR662 2.9 13.8 1.0
O A:ASP626 2.9 14.4 1.0
O A:HOH984 3.0 12.6 1.0
C A:PHE623 3.5 16.0 1.0
CB A:TYR662 3.6 14.6 1.0
CB A:PHE623 3.6 14.4 1.0
C A:TYR662 3.7 14.2 1.0
C A:VAL629 3.9 11.8 1.0
C A:ASP626 4.0 15.2 1.0
CA A:PHE623 4.2 12.4 1.0
CA A:TYR662 4.3 13.3 1.0
N A:TYR631 4.3 11.4 1.0
N A:ASP626 4.4 14.0 1.0
N A:GLU624 4.5 14.4 1.0
N A:ASN663 4.5 13.1 1.0
CA A:LEU630 4.6 11.4 1.0
CA A:GLU624 4.6 15.6 1.0
CB A:ASP626 4.6 15.0 1.0
CA A:ASP626 4.6 14.5 1.0
O A:GLU624 4.6 15.2 1.0
C A:GLU624 4.6 19.0 1.0
N A:LEU630 4.7 11.0 1.0
CB A:ASN663 4.8 10.4 1.0
CB A:TYR631 4.8 10.8 1.0
CA A:ASN663 4.8 10.8 1.0
O A:GLY659 4.9 15.4 1.0
CG A:TYR662 4.9 15.4 1.0
C A:LEU630 4.9 10.2 1.0
CG A:PHE623 4.9 12.1 1.0
CA A:VAL629 4.9 11.4 1.0

Potassium binding site 3 out of 4 in 6q0z

Go back to Potassium Binding Sites List in 6q0z
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JS28


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 Complexed with JS28 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:13.6
occ:1.00
 O B:ASP612 2.5 16.6 1.0
O B:HIS614 2.7 10.9 1.0
O B:LEU634 2.7 14.4 1.0
O B:ASP610 2.8 10.6 1.0
OD1 B:ASP610 2.8 11.6 1.0
OG B:SER633 2.8 12.1 1.0
CG B:ASP610 3.3 10.2 1.0
C B:ASP610 3.4 13.7 1.0
C B:ASP612 3.5 12.4 1.0
C B:LEU634 3.7 13.2 1.0
C B:HIS614 3.7 17.6 1.0
N B:ASP612 3.7 10.3 1.0
CB B:ASP610 3.8 10.3 1.0
N B:LEU634 3.9 15.3 1.0
CB B:SER633 3.9 11.5 1.0
CB B:HIS635 4.0 8.7 1.0
CA B:ASP612 4.0 12.6 1.0
OD2 B:ASP610 4.0 10.2 1.0
CB B:ASP612 4.2 10.0 1.0
N B:TRP611 4.2 12.3 1.0
C B:TRP611 4.2 10.5 1.0
CA B:ASP610 4.2 10.4 1.0
ND1 B:HIS635 4.3 12.3 1.0
CA B:TRP611 4.3 13.3 1.0
CA B:HIS615 4.3 15.8 1.0
CA B:SER633 4.3 11.3 1.0
N B:HIS614 4.4 10.6 1.0
N B:HIS615 4.4 15.8 1.0
CA B:HIS635 4.4 8.5 1.0
CA B:LEU634 4.4 10.5 1.0
C B:SER633 4.5 14.7 1.0
N B:HIS635 4.5 13.2 1.0
N B:GLY616 4.5 13.3 1.0
O B:HOH946 4.5 14.0 1.0
CG B:HIS635 4.6 16.6 1.0
C B:VAL613 4.6 11.2 1.0
N B:VAL613 4.7 13.6 1.0
OH B:TYR631 4.7 12.2 1.0
CA B:HIS614 4.7 11.9 1.0
C B:HIS615 4.8 17.9 1.0
CE1 B:HIS573 4.9 15.7 1.0
O B:TRP611 5.0 13.5 1.0
ND1 B:HIS573 5.0 13.4 1.0
CA B:VAL613 5.0 10.5 1.0

Potassium binding site 4 out of 4 in 6q0z

Go back to Potassium Binding Sites List in 6q0z
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JS28


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 Complexed with JS28 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:16.6
occ:1.00
 O B:HOH998 2.7 13.8 1.0
O B:PHE623 2.7 13.9 1.0
O B:VAL629 2.7 17.3 1.0
O B:TYR662 2.8 14.1 1.0
O B:HOH1007 2.9 14.4 1.0
O B:ASP626 2.9 15.1 1.0
C B:PHE623 3.6 14.0 1.0
C B:TYR662 3.6 14.7 1.0
CB B:TYR662 3.6 12.0 1.0
CB B:PHE623 3.7 12.5 1.0
C B:VAL629 3.9 13.3 1.0
C B:ASP626 4.1 15.1 1.0
CA B:TYR662 4.3 11.9 1.0
CA B:PHE623 4.3 11.3 1.0
N B:TYR631 4.4 12.4 1.0
N B:ASP626 4.5 15.7 1.0
N B:ASN663 4.5 12.2 1.0
N B:GLU624 4.5 14.7 1.0
CB B:ASP626 4.6 13.8 1.0
CA B:GLU624 4.6 16.9 1.0
CA B:LEU630 4.6 13.7 1.0
CA B:ASP626 4.6 14.1 1.0
O B:GLU624 4.6 17.4 1.0
C B:GLU624 4.6 18.3 1.0
N B:LEU630 4.7 13.4 1.0
CB B:TYR631 4.8 11.0 1.0
CB B:ASN663 4.8 12.5 1.0
CA B:ASN663 4.8 13.0 1.0
O B:GLY659 4.9 13.6 1.0
CG B:TYR662 4.9 14.3 1.0
C B:LEU630 4.9 15.5 1.0
CG B:PHE623 4.9 13.4 1.0
CA B:VAL629 5.0 15.5 1.0

Reference:

J.D.Osko, N.J.Porter, P.A.Narayana Reddy, Y.C.Xiao, J.Rokka, M.Jung, J.M.Hooker, J.M.Salvino, D.W.Christianson. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. V. 63 295 2020.
ISSN: ISSN 0022-2623
PubMed: 31793776
DOI: 10.1021/ACS.JMEDCHEM.9B01540
Page generated: Mon Aug 12 17:16:32 2024

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