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Potassium in PDB 5wgm: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083, PDB code: 5wgm 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) 49.95 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.813, 174.304, 149.064, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 18.5

Other elements in 5wgm:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
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 Acy-1083 (pdb code 5wgm). 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 Acy-1083, PDB code: 5wgm:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5wgm

Go back to Potassium Binding Sites List in 5wgm
Potassium binding site 1 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:10.2
occ:1.00
 O A:ASP612 2.6 8.8 1.0
O A:LEU634 2.6 9.0 1.0
O A:HIS614 2.7 10.0 1.0
OG A:SER633 2.7 10.4 1.0
OD1 A:ASP610 2.8 8.2 1.0
O A:ASP610 2.9 7.9 1.0
CG A:ASP610 3.3 12.8 1.0
C A:ASP610 3.5 8.4 1.0
C A:ASP612 3.6 7.3 1.0
C A:LEU634 3.7 8.8 1.0
C A:HIS614 3.7 10.3 1.0
N A:ASP612 3.8 8.3 1.0
CB A:ASP610 3.8 9.6 1.0
OD2 A:ASP610 3.9 10.7 1.0
N A:LEU634 3.9 7.4 1.0
CB A:SER633 3.9 8.5 1.0
CB A:HIS635 3.9 8.3 1.0
CA A:ASP612 4.1 8.1 1.0
N A:TRP611 4.2 6.1 1.0
CB A:ASP612 4.2 8.8 1.0
C A:TRP611 4.2 6.6 1.0
CA A:ASP610 4.3 6.7 1.0
CA A:HIS615 4.3 8.5 1.0
CA A:SER633 4.3 8.4 1.0
CA A:TRP611 4.3 6.6 1.0
ND1 A:HIS635 4.3 10.2 1.0
N A:HIS615 4.3 9.4 1.0
N A:HIS614 4.4 8.2 1.0
CA A:HIS635 4.4 7.5 1.0
C A:SER633 4.5 9.7 1.0
CA A:LEU634 4.5 7.6 1.0
O A:HOH956 4.5 10.5 1.0
N A:GLY616 4.5 10.7 1.0
N A:HIS635 4.5 8.9 1.0
CG A:HIS635 4.6 10.6 1.0
C A:VAL613 4.7 8.4 1.0
CA A:HIS614 4.7 10.9 1.0
OH A:TYR631 4.7 11.3 1.0
N A:VAL613 4.7 7.2 1.0
C A:HIS615 4.8 9.5 1.0
CE1 A:HIS573 4.8 8.8 1.0
O A:TRP611 4.9 6.7 1.0
ND1 A:HIS573 4.9 10.9 1.0

Potassium binding site 2 out of 6 in 5wgm

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Potassium binding site 2 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:22.5
occ:1.00
 O A:PHE623 2.6 13.2 1.0
O A:HOH934 2.6 16.9 1.0
O A:VAL629 2.6 15.4 1.0
O A:ASP626 2.8 18.7 1.0
O A:TYR662 3.0 13.2 1.0
O A:HOH1021 3.3 17.1 1.0
CB A:TYR662 3.5 14.8 1.0
C A:PHE623 3.5 13.2 1.0
C A:TYR662 3.7 13.8 1.0
CB A:PHE623 3.7 13.4 1.0
C A:VAL629 3.9 13.5 1.0
C A:ASP626 4.0 19.6 1.0
CA A:TYR662 4.2 15.2 1.0
CA A:PHE623 4.2 14.3 1.0
N A:ASP626 4.3 16.5 1.0
N A:GLU624 4.5 16.4 0.6
N A:GLU624 4.5 16.4 0.4
N A:TYR631 4.5 10.8 1.0
N A:ASN663 4.5 15.8 1.0
CA A:GLU624 4.5 16.6 0.6
CA A:ASP626 4.5 16.5 1.0
CA A:LEU630 4.6 9.9 1.0
CA A:GLU624 4.6 16.6 0.4
O A:GLU624 4.6 17.1 0.6
C A:GLU624 4.6 17.6 0.6
CB A:ASP626 4.6 17.1 1.0
C A:GLU624 4.7 17.7 0.4
N A:LEU630 4.7 8.6 1.0
O A:GLU624 4.7 17.1 0.4
O A:GLY659 4.8 18.2 1.0
CA A:VAL629 4.8 12.3 1.0
CG A:TYR662 4.9 14.7 1.0
CB A:ASN663 4.9 13.1 1.0
CA A:ASN663 4.9 13.5 1.0
CB A:TYR631 4.9 8.7 1.0
C A:LEU630 5.0 10.0 1.0
CG A:PHE623 5.0 12.7 1.0
CB A:VAL629 5.0 13.6 1.0

Potassium binding site 3 out of 6 in 5wgm

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Potassium binding site 3 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:10.6
occ:1.00
 O B:ASP612 2.6 7.8 1.0
O B:HIS614 2.7 11.0 1.0
OD1 B:ASP610 2.7 9.9 1.0
O B:LEU634 2.7 9.6 1.0
OG B:SER633 2.8 9.2 1.0
O B:ASP610 2.9 7.2 1.0
CG B:ASP610 3.2 11.4 1.0
C B:ASP610 3.5 9.9 1.0
C B:ASP612 3.6 9.3 1.0
C B:HIS614 3.6 9.8 1.0
C B:LEU634 3.8 9.0 1.0
N B:ASP612 3.9 9.8 1.0
CB B:ASP610 3.9 9.9 1.0
OD2 B:ASP610 3.9 12.1 1.0
N B:LEU634 4.0 10.0 1.0
CB B:SER633 4.0 9.2 1.0
CB B:HIS635 4.0 9.1 1.0
CA B:ASP612 4.1 8.9 1.0
N B:TRP611 4.2 7.1 1.0
C B:TRP611 4.2 8.2 1.0
CB B:ASP612 4.2 7.8 1.0
CA B:HIS615 4.3 10.5 1.0
CA B:ASP610 4.3 10.3 1.0
N B:HIS615 4.3 9.3 1.0
CA B:TRP611 4.3 10.5 1.0
CA B:SER633 4.3 9.1 1.0
ND1 B:HIS635 4.4 11.0 1.0
N B:HIS614 4.4 8.1 1.0
N B:GLY616 4.4 9.6 1.0
O B:HOH960 4.5 12.0 1.0
CA B:HIS635 4.5 7.5 1.0
C B:SER633 4.5 12.5 1.0
CA B:LEU634 4.5 10.8 1.0
N B:HIS635 4.6 8.1 1.0
CG B:HIS635 4.6 9.6 1.0
CA B:HIS614 4.7 10.1 1.0
C B:VAL613 4.7 9.1 1.0
OH B:TYR631 4.7 12.0 1.0
C B:HIS615 4.7 10.6 1.0
CE1 B:HIS573 4.7 9.7 1.0
N B:VAL613 4.8 7.5 1.0
ND1 B:HIS573 4.9 10.2 1.0
O B:TRP611 4.9 8.2 1.0

Potassium binding site 4 out of 6 in 5wgm

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Potassium binding site 4 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:21.9
occ:1.00
 O B:VAL629 2.6 16.0 1.0
O B:HOH984 2.6 17.3 1.0
O B:PHE623 2.6 15.4 1.0
O B:ASP626 2.8 18.6 1.0
O B:TYR662 3.0 13.1 1.0
O B:HOH959 3.3 14.1 1.0
CB B:TYR662 3.5 16.1 1.0
C B:PHE623 3.6 14.1 1.0
C B:TYR662 3.7 15.3 1.0
CB B:PHE623 3.7 14.2 1.0
C B:VAL629 3.8 15.0 1.0
C B:ASP626 4.0 20.3 1.0
CA B:TYR662 4.2 16.4 1.0
CA B:PHE623 4.3 12.9 1.0
N B:ASP626 4.4 17.1 1.0
N B:TYR631 4.5 10.3 1.0
N B:ASN663 4.5 16.3 1.0
CA B:LEU630 4.5 7.9 1.0
CA B:ASP626 4.6 16.3 1.0
CB B:ASP626 4.6 17.5 1.0
N B:GLU624 4.6 12.9 1.0
N B:LEU630 4.6 10.1 1.0
CA B:GLU624 4.6 14.5 1.0
O B:GLU624 4.7 17.6 1.0
C B:GLU624 4.7 13.7 1.0
CG B:TYR662 4.8 17.1 1.0
O B:GLY659 4.8 18.1 1.0
CA B:VAL629 4.8 13.7 1.0
CA B:ASN663 4.9 16.5 1.0
CB B:TYR631 4.9 9.7 1.0
C B:LEU630 4.9 13.1 1.0
CB B:ASN663 4.9 16.3 1.0
CG B:PHE623 5.0 13.5 1.0
N B:VAL629 5.0 12.4 1.0
CB B:VAL629 5.0 14.9 1.0

Potassium binding site 5 out of 6 in 5wgm

Go back to Potassium Binding Sites List in 5wgm
Potassium binding site 5 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K802

b:10.5
occ:1.00
 O C:ASP612 2.6 8.4 1.0
O C:LEU634 2.7 9.3 1.0
O C:HIS614 2.7 9.2 1.0
OD1 C:ASP610 2.8 10.1 1.0
OG C:SER633 2.8 10.2 1.0
O C:ASP610 2.8 8.6 1.0
CG C:ASP610 3.3 12.7 1.0
C C:ASP610 3.5 9.4 1.0
C C:ASP612 3.6 7.5 1.0
C C:HIS614 3.7 9.9 1.0
C C:LEU634 3.7 11.2 1.0
N C:ASP612 3.8 8.6 1.0
CB C:ASP610 3.9 10.0 1.0
CB C:SER633 3.9 10.7 1.0
OD2 C:ASP610 3.9 11.9 1.0
N C:LEU634 3.9 9.6 1.0
CB C:HIS635 4.0 9.5 1.0
CA C:ASP612 4.1 7.6 1.0
C C:TRP611 4.2 9.5 1.0
N C:TRP611 4.2 7.8 1.0
CB C:ASP612 4.2 11.9 1.0
CA C:ASP610 4.3 8.4 1.0
CA C:HIS615 4.3 11.6 1.0
CA C:TRP611 4.3 6.8 1.0
CA C:SER633 4.3 9.1 1.0
N C:HIS615 4.4 9.7 1.0
ND1 C:HIS635 4.4 12.4 1.0
N C:HIS614 4.4 8.1 1.0
N C:GLY616 4.5 11.3 1.0
CA C:HIS635 4.5 8.0 1.0
C C:SER633 4.5 10.3 1.0
CA C:LEU634 4.5 8.7 1.0
O C:HOH933 4.6 10.5 1.0
N C:HIS635 4.6 9.9 1.0
OH C:TYR631 4.7 10.1 1.0
CG C:HIS635 4.7 11.3 1.0
C C:VAL613 4.7 9.8 1.0
CA C:HIS614 4.7 10.2 1.0
N C:VAL613 4.7 9.3 1.0
C C:HIS615 4.7 11.4 1.0
CE1 C:HIS573 4.8 11.4 1.0
O C:TRP611 4.9 8.4 1.0
ND1 C:HIS573 4.9 12.0 1.0

Potassium binding site 6 out of 6 in 5wgm

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Potassium binding site 6 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K803

b:23.8
occ:1.00
 O C:HOH992 2.6 19.0 1.0
O C:VAL629 2.6 15.5 1.0
O C:PHE623 2.6 14.5 1.0
O C:ASP626 2.9 21.8 1.0
O C:TYR662 2.9 13.3 1.0
O C:HOH1012 3.4 16.2 1.0
CB C:TYR662 3.6 15.0 1.0
C C:PHE623 3.6 13.8 1.0
C C:TYR662 3.7 12.5 1.0
CB C:PHE623 3.7 13.3 1.0
C C:VAL629 3.8 14.6 1.0
C C:ASP626 4.0 21.7 1.0
CA C:TYR662 4.3 16.8 1.0
CA C:PHE623 4.3 14.8 1.0
N C:ASP626 4.4 21.4 1.0
N C:TYR631 4.5 12.1 1.0
N C:ASN663 4.5 14.5 1.0
N C:GLU624 4.5 16.1 0.3
N C:GLU624 4.5 16.1 0.7
CA C:LEU630 4.5 12.7 1.0
CA C:GLU624 4.6 16.6 0.3
CA C:GLU624 4.6 16.6 0.7
CA C:ASP626 4.6 21.7 1.0
O C:GLU624 4.6 19.2 0.7
N C:LEU630 4.6 12.5 1.0
CB C:ASP626 4.7 18.9 1.0
C C:GLU624 4.7 16.9 0.7
C C:GLU624 4.7 17.0 0.3
O C:GLU624 4.7 19.2 0.3
CA C:VAL629 4.8 14.3 1.0
O C:GLY659 4.8 19.3 1.0
CG C:TYR662 4.8 18.8 1.0
CA C:ASN663 4.9 13.9 1.0
CB C:TYR631 4.9 9.2 1.0
CB C:VAL629 4.9 14.4 1.0
C C:LEU630 4.9 12.4 1.0
CB C:ASN663 4.9 14.2 1.0

Reference:

N.J.Porter, A.Mahendran, R.Breslow, D.W.Christianson. Unusual Zinc-Binding Mode of HDAC6-Selective Hydroxamate Inhibitors. Proc. Natl. Acad. Sci. V. 114 13459 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29203661
DOI: 10.1073/PNAS.1718823114
Page generated: Mon Aug 12 14:56:10 2024

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