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Potassium in PDB 6pye: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160, PDB code: 6pye 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) 60.32 / 1.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.000, 83.130, 88.590, 90.00, 98.33, 90.00
R / Rfree (%) 16.4 / 18.2

Other elements in 6pye:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160 also contains other interesting chemical elements:

Fluorine (F) 6 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 NR160 (pdb code 6pye). 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 NR160, PDB code: 6pye:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6pye

Go back to Potassium Binding Sites List in 6pye
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 NR160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K805

b:5.4
occ:0.86
 O A:ASP612 2.6 6.3 1.0
O A:HIS614 2.7 6.0 1.0
O A:LEU634 2.7 6.6 1.0
OG A:SER633 2.8 6.8 1.0
OD1 A:ASP610 2.8 6.4 1.0
O A:ASP610 2.8 6.4 1.0
CG A:ASP610 3.3 7.4 1.0
C A:ASP610 3.5 6.6 1.0
C A:ASP612 3.6 6.5 1.0
C A:HIS614 3.7 4.8 1.0
C A:LEU634 3.7 5.4 1.0
CB A:ASP610 3.8 7.6 1.0
N A:ASP612 3.9 6.5 1.0
OD2 A:ASP610 3.9 7.3 1.0
N A:LEU634 3.9 5.9 1.0
CB A:SER633 4.0 5.3 1.0
CB A:HIS635 4.0 6.1 1.0
CA A:ASP612 4.1 4.8 1.0
CB A:ASP612 4.2 7.5 1.0
N A:TRP611 4.2 5.1 1.0
C A:TRP611 4.2 5.8 1.0
CA A:ASP610 4.3 5.0 1.0
CA A:HIS615 4.3 4.7 1.0
CA A:SER633 4.3 5.2 1.0
ND1 A:HIS635 4.3 7.0 1.0
N A:HIS615 4.4 6.1 1.0
CA A:TRP611 4.4 6.4 1.0
N A:HIS614 4.4 4.9 1.0
C A:SER633 4.5 6.8 1.0
CA A:HIS635 4.5 5.1 1.0
N A:GLY616 4.5 5.3 1.0
CA A:LEU634 4.5 6.5 1.0
O A:HOH931 4.5 8.8 1.0
N A:HIS635 4.5 5.9 1.0
CG A:HIS635 4.6 6.2 1.0
OH A:TYR631 4.7 6.2 1.0
C A:VAL613 4.7 5.4 1.0
CA A:HIS614 4.7 7.0 1.0
N A:VAL613 4.7 6.7 1.0
C A:HIS615 4.8 5.2 1.0
CE1 A:HIS573 4.8 8.8 1.0
ND1 A:HIS573 4.9 8.1 1.0
O A:TRP611 4.9 6.4 1.0

Potassium binding site 2 out of 4 in 6pye

Go back to Potassium Binding Sites List in 6pye
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 NR160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K806

b:8.9
occ:0.76
 O A:VAL629 2.7 9.6 1.0
O A:PHE623 2.7 8.7 1.0
O A:HOH1057 2.8 10.1 1.0
O A:TYR662 2.8 7.0 1.0
O A:ASP626 2.9 11.7 1.0
O A:HOH1027 3.0 9.3 1.0
C A:TYR662 3.6 8.2 1.0
CB A:TYR662 3.6 8.0 1.0
C A:PHE623 3.7 8.2 1.0
CB A:PHE623 3.7 7.2 1.0
C A:VAL629 3.9 7.4 1.0
C A:ASP626 4.1 11.2 1.0
CA A:TYR662 4.2 7.3 1.0
N A:TYR631 4.3 5.5 1.0
CA A:PHE623 4.3 8.1 1.0
N A:ASN663 4.4 7.5 1.0
N A:ASP626 4.5 10.7 1.0
CA A:LEU630 4.5 7.0 1.0
N A:GLU624 4.6 9.0 1.0
CA A:GLU624 4.6 9.1 1.0
N A:LEU630 4.7 6.2 1.0
CA A:ASP626 4.7 9.4 1.0
O A:GLU624 4.7 10.6 1.0
CB A:ASP626 4.7 9.8 1.0
C A:GLU624 4.7 10.5 1.0
CB A:TYR631 4.7 6.0 1.0
CA A:ASN663 4.7 5.7 1.0
CB A:ASN663 4.8 5.7 1.0
C A:LEU630 4.8 5.6 1.0
CG A:TYR662 4.9 10.0 1.0
CA A:VAL629 4.9 8.1 1.0
O A:GLY659 5.0 10.6 1.0
CG A:PHE623 5.0 7.6 1.0
OD1 A:ASN663 5.0 8.3 1.0

Potassium binding site 3 out of 4 in 6pye

Go back to Potassium Binding Sites List in 6pye
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 NR160 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K808

b:11.3
occ:1.00
 O B:ASP612 2.6 9.6 1.0
O B:HIS614 2.7 10.1 1.0
OD1 B:ASP610 2.7 9.5 1.0
OG B:SER633 2.7 10.8 1.0
O B:LEU634 2.7 12.2 1.0
O B:ASP610 2.8 9.7 1.0
CG B:ASP610 3.3 8.1 1.0
C B:ASP610 3.5 10.4 1.0
C B:ASP612 3.6 8.2 1.0
C B:HIS614 3.7 10.0 1.0
C B:LEU634 3.7 12.7 1.0
CB B:ASP610 3.8 9.4 1.0
N B:ASP612 3.8 9.3 1.0
CB B:SER633 3.9 10.7 1.0
N B:LEU634 4.0 9.9 1.0
OD2 B:ASP610 4.0 10.4 1.0
CB B:HIS635 4.0 11.5 1.0
CA B:ASP612 4.1 8.0 1.0
CB B:ASP612 4.2 9.2 1.0
C B:TRP611 4.2 7.9 1.0
N B:TRP611 4.2 10.1 1.0
CA B:HIS615 4.3 11.0 1.0
CA B:ASP610 4.3 8.5 1.0
CA B:SER633 4.3 10.8 1.0
N B:HIS615 4.3 11.4 1.0
ND1 B:HIS635 4.3 13.3 1.0
CA B:TRP611 4.4 8.7 1.0
N B:HIS614 4.4 9.1 1.0
N B:GLY616 4.4 9.6 1.0
CA B:HIS635 4.5 9.7 1.0
C B:SER633 4.5 12.0 1.0
O B:HOH946 4.5 12.9 1.0
CA B:LEU634 4.5 10.4 1.0
N B:HIS635 4.6 10.1 1.0
CG B:HIS635 4.6 12.0 1.0
OH B:TYR631 4.7 11.0 1.0
C B:VAL613 4.7 9.7 1.0
CA B:HIS614 4.7 10.7 1.0
N B:VAL613 4.7 8.1 1.0
C B:HIS615 4.7 9.2 1.0
CE1 B:HIS573 4.8 11.0 1.0
O B:TRP611 4.9 10.5 1.0
ND1 B:HIS573 4.9 9.5 1.0

Potassium binding site 4 out of 4 in 6pye

Go back to Potassium Binding Sites List in 6pye
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 NR160 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K809

b:14.7
occ:0.78
 O B:VAL629 2.7 16.0 1.0
O B:HOH1009 2.7 16.5 1.0
O B:PHE623 2.7 16.6 1.0
O B:TYR662 2.8 13.9 1.0
O B:ASP626 2.9 19.9 1.0
O B:HOH1012 3.0 13.2 1.0
C B:TYR662 3.5 16.7 1.0
CB B:TYR662 3.6 13.6 1.0
C B:PHE623 3.7 13.9 1.0
CB B:PHE623 3.8 14.1 1.0
C B:VAL629 3.9 10.7 1.0
C B:ASP626 4.1 17.1 1.0
CA B:TYR662 4.2 14.0 1.0
N B:TYR631 4.3 9.0 1.0
CA B:PHE623 4.4 14.5 1.0
N B:ASN663 4.4 16.1 1.0
N B:ASP626 4.5 18.4 1.0
CA B:LEU630 4.5 10.8 1.0
N B:GLU624 4.6 16.2 1.0
CA B:GLU624 4.6 17.1 1.0
CB B:ASP626 4.7 17.1 1.0
N B:LEU630 4.7 9.2 1.0
CA B:ASP626 4.7 16.0 1.0
CB B:TYR631 4.7 10.7 1.0
O B:GLU624 4.7 15.8 1.0
C B:GLU624 4.7 15.3 1.0
CA B:ASN663 4.7 13.5 1.0
CB B:ASN663 4.7 12.4 1.0
C B:LEU630 4.9 11.2 1.0
CA B:VAL629 4.9 13.6 1.0
O B:GLY659 5.0 16.7 1.0
CG B:TYR662 5.0 17.2 1.0

Reference:

N.Ressing, M.Sonnichsen, J.D.Osko, A.Scholer, J.Schliehe-Diecks, A.Skerhut, A.Borkhardt, J.Hauer, M.U.Kassack, D.W.Christianson, S.Bhatia, F.K.Hansen. Multicomponent Synthesis, Binding Mode, and Structure-Activity Relationship of Selective Histone Deacetylase 6 (HDAC6) Inhibitors with Bifurcated Capping Groups. J.Med.Chem. V. 63 10339 2020.
ISSN: ISSN 0022-2623
PubMed: 32803970
DOI: 10.1021/ACS.JMEDCHEM.9B01888
Page generated: Mon Aug 12 17:14:03 2024

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