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Potassium in PDB 5w5k: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70, PDB code: 5w5k was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.14 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 101.290, 170.940, 151.370, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 22

Other elements in 5w5k:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70 also contains other interesting chemical elements:

Zinc (Zn) 3 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 KV70 (pdb code 5w5k). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70, PDB code: 5w5k:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5w5k

Go back to Potassium Binding Sites List in 5w5k
Potassium binding site 1 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


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 KV70 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:12.4
occ:1.00
 O A:HIS614 2.8 13.0 1.0
OG A:SER633 2.8 10.1 1.0
O A:ASP610 2.8 10.9 1.0
O A:LEU634 2.8 13.6 1.0
O A:ASP612 2.8 15.5 1.0
OD1 A:ASP610 2.9 12.1 1.0
CG A:ASP610 3.2 11.6 1.0
C A:ASP610 3.4 12.1 1.0
CB A:ASP610 3.6 9.9 1.0
C A:HIS614 3.8 16.1 1.0
C A:LEU634 3.8 12.8 1.0
C A:ASP612 3.8 13.4 1.0
OD2 A:ASP610 3.8 13.6 1.0
CB A:SER633 3.9 10.2 1.0
N A:ASP612 3.9 11.5 1.0
N A:LEU634 4.0 12.4 1.0
CB A:HIS635 4.1 12.8 1.0
CA A:ASP610 4.1 12.4 1.0
N A:TRP611 4.2 9.6 1.0
CA A:HIS615 4.2 13.1 1.0
CA A:ASP612 4.2 12.3 1.0
CA A:SER633 4.3 11.0 1.0
N A:GLY616 4.3 16.7 1.0
C A:TRP611 4.3 11.1 1.0
CB A:ASP612 4.3 13.9 1.0
N A:HIS615 4.4 15.6 1.0
CA A:TRP611 4.4 11.9 1.0
C A:SER633 4.5 12.9 1.0
ND1 A:HIS635 4.5 13.3 1.0
CA A:LEU634 4.6 12.3 1.0
C A:HIS615 4.6 15.4 1.0
CA A:HIS635 4.6 13.0 1.0
N A:HIS614 4.7 12.3 1.0
N A:HIS635 4.7 11.9 1.0
O A:HOH915 4.7 11.0 1.0
OH A:TYR631 4.7 14.2 1.0
CG A:HIS635 4.8 11.5 1.0
CA A:HIS614 4.9 13.5 1.0
C A:VAL613 4.9 12.7 1.0
N A:VAL613 5.0 13.3 1.0
ND1 A:HIS573 5.0 12.7 1.0

Potassium binding site 2 out of 6 in 5w5k

Go back to Potassium Binding Sites List in 5w5k
Potassium binding site 2 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


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 KV70 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:14.1
occ:1.00
 O A:PHE623 2.7 21.6 1.0
O A:VAL629 2.7 15.8 1.0
O A:TYR662 2.8 16.0 1.0
O A:HOH909 2.8 18.5 1.0
O A:ASP626 2.9 19.6 1.0
O A:HOH948 3.0 16.6 1.0
C A:TYR662 3.6 16.4 1.0
CB A:TYR662 3.7 16.6 1.0
C A:PHE623 3.7 19.9 1.0
CB A:PHE623 3.8 17.5 1.0
C A:VAL629 4.0 15.8 1.0
C A:ASP626 4.1 20.1 1.0
CA A:TYR662 4.2 17.5 1.0
N A:TYR631 4.3 13.1 1.0
N A:ASN663 4.4 16.1 1.0
CA A:PHE623 4.4 16.2 1.0
N A:ASP626 4.5 21.4 1.0
CA A:LEU630 4.6 14.4 1.0
N A:GLU624 4.6 20.4 1.0
CA A:GLU624 4.6 19.6 1.0
CA A:ASP626 4.7 19.1 1.0
CB A:TYR631 4.7 13.2 1.0
CA A:ASN663 4.7 16.0 1.0
CB A:ASN663 4.7 15.1 1.0
O A:GLU624 4.7 21.5 1.0
C A:GLU624 4.7 21.0 1.0
N A:LEU630 4.7 15.0 1.0
CB A:ASP626 4.8 19.5 1.0
C A:LEU630 4.9 12.9 1.0
CG A:TYR662 5.0 17.6 1.0
O A:GLY659 5.0 22.4 1.0

Potassium binding site 3 out of 6 in 5w5k

Go back to Potassium Binding Sites List in 5w5k
Potassium binding site 3 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


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 KV70 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:13.7
occ:1.00
 OG B:SER633 2.7 13.1 1.0
O B:LEU634 2.8 14.7 1.0
O B:HIS614 2.8 14.9 1.0
O B:ASP612 2.8 12.2 1.0
OD1 B:ASP610 2.8 11.7 1.0
O B:ASP610 2.8 11.7 1.0
CG B:ASP610 3.1 12.1 1.0
C B:ASP610 3.5 10.6 1.0
CB B:ASP610 3.6 10.3 1.0
OD2 B:ASP610 3.7 13.8 1.0
C B:LEU634 3.7 13.7 1.0
C B:ASP612 3.8 12.5 1.0
C B:HIS614 3.8 15.1 1.0
CB B:SER633 3.8 11.0 1.0
N B:ASP612 3.9 12.7 1.0
N B:LEU634 4.0 11.2 1.0
CB B:HIS635 4.0 14.7 1.0
CA B:ASP610 4.1 11.0 1.0
CA B:ASP612 4.2 13.3 1.0
N B:TRP611 4.2 10.0 1.0
CA B:SER633 4.2 12.9 1.0
CB B:ASP612 4.3 14.3 1.0
CA B:HIS615 4.3 12.3 1.0
N B:GLY616 4.3 13.5 1.0
C B:TRP611 4.3 12.0 1.0
ND1 B:HIS635 4.4 14.8 1.0
N B:HIS615 4.4 13.5 1.0
CA B:TRP611 4.5 10.5 1.0
OH B:TYR631 4.5 14.8 1.0
C B:SER633 4.5 12.1 1.0
CA B:LEU634 4.5 11.0 1.0
CA B:HIS635 4.6 12.2 1.0
N B:HIS635 4.6 11.5 1.0
N B:HIS614 4.6 14.9 1.0
C B:HIS615 4.7 15.6 1.0
CG B:HIS635 4.7 14.2 1.0
O B:HOH914 4.8 11.6 1.0
CA B:HIS614 4.9 14.6 1.0
N B:VAL613 4.9 11.1 1.0
C B:VAL613 4.9 13.8 1.0
ND1 B:HIS573 5.0 12.9 1.0

Potassium binding site 4 out of 6 in 5w5k

Go back to Potassium Binding Sites List in 5w5k
Potassium binding site 4 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


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 KV70 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:21.4
occ:1.00
 O B:PHE623 2.7 20.5 1.0
O B:TYR662 2.7 19.4 1.0
O B:VAL629 2.8 15.8 1.0
O B:HOH908 2.9 22.7 1.0
O B:ASP626 3.0 23.9 1.0
O B:HOH909 3.1 17.6 1.0
C B:TYR662 3.5 16.8 1.0
CB B:TYR662 3.6 20.7 1.0
C B:PHE623 3.6 20.2 1.0
CB B:PHE623 4.0 17.8 1.0
C B:VAL629 4.0 18.0 1.0
C B:ASP626 4.1 22.1 1.0
CA B:TYR662 4.1 19.6 1.0
N B:ASN663 4.3 18.7 1.0
CA B:GLU624 4.3 22.8 1.0
N B:TYR631 4.3 12.2 1.0
N B:GLU624 4.4 19.7 1.0
CA B:PHE623 4.4 19.0 1.0
N B:ASP626 4.5 21.7 1.0
O B:GLU624 4.5 19.9 1.0
C B:GLU624 4.5 23.0 1.0
CA B:LEU630 4.5 15.3 1.0
CB B:ASN663 4.6 16.7 1.0
CA B:ASN663 4.6 16.8 1.0
CA B:ASP626 4.7 19.6 1.0
N B:LEU630 4.7 17.0 1.0
CB B:ASP626 4.8 19.6 1.0
O B:GLY659 4.8 23.3 1.0
CB B:TYR631 4.8 12.4 1.0
CG B:TYR662 4.9 22.4 1.0
C B:LEU630 4.9 14.3 1.0

Potassium binding site 5 out of 6 in 5w5k

Go back to Potassium Binding Sites List in 5w5k
Potassium binding site 5 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K802

b:12.8
occ:1.00
 OG C:SER633 2.7 11.2 1.0
O C:HIS614 2.8 18.8 1.0
O C:ASP612 2.8 17.4 1.0
O C:ASP610 2.8 16.1 1.0
O C:LEU634 2.8 15.8 1.0
OD1 C:ASP610 2.8 16.0 1.0
CG C:ASP610 3.1 15.0 1.0
C C:ASP610 3.4 13.3 1.0
CB C:ASP610 3.6 13.4 1.0
C C:ASP612 3.7 14.4 1.0
OD2 C:ASP610 3.8 15.8 1.0
C C:LEU634 3.8 16.9 1.0
C C:HIS614 3.8 17.8 1.0
CB C:SER633 3.8 12.5 1.0
N C:ASP612 3.8 12.9 1.0
N C:LEU634 3.9 13.5 1.0
CA C:ASP610 4.1 12.4 1.0
CB C:HIS635 4.1 16.0 1.0
N C:TRP611 4.1 13.4 1.0
CA C:ASP612 4.1 14.8 1.0
CA C:SER633 4.2 14.5 1.0
CB C:ASP612 4.2 16.0 1.0
C C:TRP611 4.2 14.1 1.0
CA C:HIS615 4.3 17.7 1.0
N C:GLY616 4.4 14.8 1.0
CA C:TRP611 4.4 14.2 1.0
C C:SER633 4.5 14.8 1.0
ND1 C:HIS635 4.5 17.5 1.0
N C:HIS615 4.5 16.0 1.0
OH C:TYR631 4.5 16.1 1.0
CA C:LEU634 4.5 13.4 1.0
N C:HIS614 4.6 13.9 1.0
N C:HIS635 4.7 15.7 1.0
CA C:HIS635 4.7 14.7 1.0
O C:HOH922 4.7 13.1 1.0
C C:HIS615 4.7 17.2 1.0
CG C:HIS635 4.8 16.1 1.0
CA C:HIS614 4.9 14.3 1.0
N C:VAL613 4.9 14.7 1.0
C C:VAL613 4.9 14.2 1.0
ND1 C:HIS573 5.0 13.9 1.0

Potassium binding site 6 out of 6 in 5w5k

Go back to Potassium Binding Sites List in 5w5k
Potassium binding site 6 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with KV70 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K803

b:25.6
occ:1.00
 O C:PHE623 2.7 22.3 1.0
O C:TYR662 2.7 21.6 1.0
O C:VAL629 2.8 20.0 1.0
O C:HOH902 2.8 26.5 1.0
O C:ASP626 2.9 25.6 1.0
O C:HOH901 3.3 19.8 1.0
C C:TYR662 3.4 21.2 1.0
CB C:TYR662 3.5 25.2 1.0
C C:PHE623 3.7 22.0 1.0
C C:VAL629 4.0 17.9 1.0
CB C:PHE623 4.0 21.2 1.0
C C:ASP626 4.1 25.1 1.0
CA C:TYR662 4.1 23.8 1.0
N C:ASN663 4.2 19.5 1.0
N C:TYR631 4.3 15.1 1.0
CA C:GLU624 4.4 28.8 1.0
N C:ASP626 4.4 26.6 1.0
O C:GLU624 4.4 33.5 1.0
N C:GLU624 4.5 27.1 1.0
C C:GLU624 4.5 29.9 1.0
CA C:PHE623 4.5 21.2 1.0
CA C:LEU630 4.5 15.8 1.0
CB C:ASN663 4.6 18.5 1.0
CA C:ASN663 4.6 17.9 1.0
CA C:ASP626 4.7 24.7 1.0
O C:GLY659 4.7 30.4 1.0
N C:LEU630 4.7 16.1 1.0
CB C:ASP626 4.8 21.7 1.0
CG C:TYR662 4.8 26.5 1.0
CB C:TYR631 4.8 13.8 1.0
C C:LEU630 4.9 16.2 1.0

Reference:

K.Vogerl, N.Ong, J.Senger, D.Herp, K.Schmidtkunz, M.Marek, M.Muller, K.Bartel, T.B.Shaik, N.J.Porter, D.Robaa, D.W.Christianson, C.Romier, W.Sippl, M.Jung, F.Bracher. Synthesis and Biological Investigation of Phenothiazine-Based Benzhydroxamic Acids As Selective Histone Deacetylase 6 Inhibitors. J.Med.Chem. V. 62 1138 2019.
ISSN: ISSN 0022-2623
PubMed: 30645113
DOI: 10.1021/ACS.JMEDCHEM.8B01090
Page generated: Mon Aug 12 14:52:46 2024

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