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Potassium in PDB 7jom: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317, PDB code: 7jom was solved by P.R.Watson, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.43 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.46, 96.45, 96.45, 90, 90, 90
R / Rfree (%) 16.8 / 20.7

Other elements in 7jom:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 also contains other interesting chemical elements:

Fluorine (F) 8 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 to-317 (pdb code 7jom). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317, PDB code: 7jom:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 7jom

Go back to Potassium Binding Sites List in 7jom
Potassium binding site 1 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317


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 to-317 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K908

b:6.8
occ:1.00
 O A:ASP612 2.6 4.8 1.0
O A:HIS614 2.7 5.7 1.0
O A:LEU634 2.7 7.6 1.0
OG A:SER633 2.8 7.1 1.0
OD1 A:ASP610 2.8 6.4 1.0
O A:ASP610 2.8 4.5 1.0
CG A:ASP610 3.3 6.3 1.0
C A:ASP610 3.5 5.4 1.0
C A:ASP612 3.6 4.9 1.0
C A:HIS614 3.7 5.7 1.0
C A:LEU634 3.7 8.0 1.0
CB A:ASP610 3.8 5.3 1.0
N A:ASP612 3.8 4.6 1.0
OD2 A:ASP610 3.9 8.4 1.0
N A:LEU634 3.9 6.5 1.0
CB A:SER633 4.0 4.4 1.0
CB A:HIS635 4.1 5.5 1.0
CA A:ASP612 4.1 6.4 1.0
C A:TRP611 4.2 5.0 1.0
N A:TRP611 4.2 5.3 1.0
CB A:ASP612 4.2 5.3 1.0
CA A:ASP610 4.2 3.9 1.0
CA A:HIS615 4.3 7.5 1.0
CA A:TRP611 4.3 6.6 1.0
CA A:SER633 4.3 5.5 1.0
N A:HIS615 4.4 5.2 1.0
ND1 A:HIS635 4.4 9.4 1.0
N A:GLY616 4.5 6.6 1.0
N A:HIS614 4.5 4.7 1.0
O A:HOH1046 4.5 7.2 1.0
CA A:LEU634 4.5 7.5 1.0
C A:SER633 4.5 7.6 1.0
CA A:HIS635 4.5 6.3 1.0
N A:HIS635 4.6 7.9 1.0
C A:VAL613 4.7 5.5 1.0
CG A:HIS635 4.7 7.0 1.0
N A:VAL613 4.7 4.3 1.0
C A:HIS615 4.7 7.0 1.0
OH A:TYR631 4.7 6.2 1.0
CA A:HIS614 4.7 4.8 1.0
O A:TRP611 4.9 7.2 1.0
CE1 A:HIS573 4.9 4.9 1.0

Potassium binding site 2 out of 5 in 7jom

Go back to Potassium Binding Sites List in 7jom
Potassium binding site 2 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317


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 to-317 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K909

b:7.5
occ:1.00
 O A:PHE623 2.7 8.1 1.0
O A:VAL629 2.7 7.4 1.0
O A:HOH1078 2.7 7.4 1.0
O A:TYR662 2.8 6.3 1.0
O A:ASP626 2.9 8.7 1.0
O A:HOH1107 3.0 6.2 1.0
C A:TYR662 3.6 8.2 1.0
C A:PHE623 3.6 7.8 1.0
CB A:TYR662 3.7 9.6 1.0
CB A:PHE623 3.7 5.2 1.0
C A:VAL629 3.9 5.5 1.0
C A:ASP626 4.0 12.6 1.0
CA A:TYR662 4.3 7.7 1.0
N A:TYR631 4.3 4.4 1.0
CA A:PHE623 4.3 7.1 1.0
N A:ASP626 4.5 6.9 1.0
N A:ASN663 4.5 7.0 1.0
N A:GLU624 4.5 6.9 1.0
CA A:GLU624 4.5 5.9 1.0
CA A:ASP626 4.6 10.4 1.0
CA A:LEU630 4.6 5.7 1.0
CB A:ASP626 4.7 8.6 1.0
O A:GLU624 4.7 8.9 1.0
C A:GLU624 4.7 7.3 1.0
CB A:TYR631 4.7 4.3 1.0
N A:LEU630 4.7 5.8 1.0
CB A:ASN663 4.8 6.1 1.0
CA A:ASN663 4.8 9.2 1.0
O A:GLY659 4.9 9.0 1.0
C A:LEU630 4.9 7.1 1.0
CA A:VAL629 4.9 6.2 1.0

Potassium binding site 3 out of 5 in 7jom

Go back to Potassium Binding Sites List in 7jom
Potassium binding site 3 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317


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 to-317 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K910

b:38.8
occ:1.00
 O1 A:FMT904 2.3 23.7 1.0
OE1 A:GLU624 2.8 15.2 1.0
C A:FMT904 2.8 28.0 1.0
NE2 A:HIS621 3.0 11.8 1.0
CD2 A:HIS621 3.0 12.6 1.0
O2 A:FMT904 3.1 27.6 1.0
OE2 A:GLU624 3.1 14.5 1.0
CD A:GLU624 3.3 15.3 1.0
NE2 A:GLN620 3.4 9.3 1.0
OD2 A:ASP648 3.4 10.0 1.0
CG A:ASP648 3.5 12.8 1.0
OD1 A:ASP648 3.8 13.4 1.0
CB A:ASP648 3.9 9.9 1.0
O A:HOH1007 4.0 24.1 1.0
CE1 A:HIS621 4.3 9.8 1.0
CG A:HIS621 4.4 9.6 1.0
CD A:GLN620 4.5 7.8 1.0
CG A:GLN620 4.7 6.9 1.0
CA A:ASP648 4.7 10.8 1.0
CG A:GLU624 4.9 8.6 1.0
ND1 A:HIS621 5.0 7.4 1.0

Potassium binding site 4 out of 5 in 7jom

Go back to Potassium Binding Sites List in 7jom
Potassium binding site 4 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317


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 to-317 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K805

b:8.4
occ:1.00
 O B:PHE623 2.6 6.1 1.0
O B:VAL629 2.7 7.8 1.0
O B:HOH957 2.7 5.6 1.0
O B:TYR662 2.8 6.0 1.0
O B:HOH1031 2.8 5.9 1.0
O B:ASP626 2.9 10.6 1.0
C B:PHE623 3.6 8.1 1.0
C B:TYR662 3.6 6.9 1.0
CB B:TYR662 3.7 8.7 1.0
CB B:PHE623 3.8 5.9 1.0
C B:VAL629 3.9 5.2 1.0
C B:ASP626 4.0 11.3 1.0
CA B:TYR662 4.3 7.5 1.0
N B:TYR631 4.3 5.2 1.0
CA B:PHE623 4.3 6.8 1.0
N B:ASN663 4.4 7.5 1.0
N B:ASP626 4.4 8.8 1.0
N B:GLU624 4.5 6.8 1.0
CA B:GLU624 4.5 5.8 1.0
CA B:LEU630 4.6 5.1 1.0
CA B:ASP626 4.6 8.2 1.0
O B:GLU624 4.6 8.2 1.0
C B:GLU624 4.6 8.0 1.0
CB B:ASP626 4.7 10.1 1.0
N B:LEU630 4.7 5.2 1.0
CB B:TYR631 4.7 4.4 1.0
CA B:ASN663 4.8 8.3 1.0
CB B:ASN663 4.8 5.4 1.0
C B:LEU630 4.9 5.7 1.0
O B:GLY659 4.9 9.6 1.0
CA B:VAL629 4.9 5.2 1.0

Potassium binding site 5 out of 5 in 7jom

Go back to Potassium Binding Sites List in 7jom
Potassium binding site 5 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317


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 Complexed with to-317 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K806

b:7.4
occ:1.00
 O B:ASP612 2.6 5.3 1.0
O B:LEU634 2.7 7.9 1.0
O B:HIS614 2.7 5.5 1.0
OG B:SER633 2.7 7.3 1.0
OD1 B:ASP610 2.8 7.1 1.0
O B:ASP610 2.9 6.0 1.0
CG B:ASP610 3.2 6.0 1.0
C B:ASP610 3.5 5.9 1.0
C B:ASP612 3.6 7.3 1.0
C B:HIS614 3.7 5.9 1.0
C B:LEU634 3.7 6.1 1.0
CB B:ASP610 3.8 6.1 1.0
N B:ASP612 3.8 5.0 1.0
OD2 B:ASP610 3.9 7.4 1.0
CB B:HIS635 4.0 6.0 1.0
N B:LEU634 4.0 8.1 1.0
CB B:SER633 4.0 3.9 1.0
CA B:ASP612 4.1 6.3 1.0
C B:TRP611 4.2 7.3 1.0
N B:TRP611 4.2 5.4 1.0
CB B:ASP612 4.2 5.2 1.0
CA B:ASP610 4.3 5.9 1.0
CA B:TRP611 4.3 5.9 1.0
CA B:HIS615 4.3 6.9 1.0
CA B:SER633 4.4 5.5 1.0
N B:HIS615 4.4 4.8 1.0
N B:HIS614 4.4 5.2 1.0
O B:HOH940 4.5 8.1 1.0
ND1 B:HIS635 4.5 7.4 1.0
CA B:HIS635 4.5 7.1 1.0
N B:GLY616 4.5 6.3 1.0
CA B:LEU634 4.5 9.3 1.0
C B:SER633 4.6 7.2 1.0
N B:HIS635 4.6 7.6 1.0
C B:VAL613 4.6 8.0 1.0
CA B:HIS614 4.7 5.6 1.0
CG B:HIS635 4.7 8.0 1.0
N B:VAL613 4.7 3.8 1.0
OH B:TYR631 4.7 6.5 1.0
C B:HIS615 4.8 6.5 1.0
CE1 B:HIS573 4.9 6.2 1.0
O B:TRP611 4.9 6.4 1.0
ND1 B:HIS573 5.0 7.4 1.0

Reference:

P.R.Watson, D.W.Christianson. Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with to-317 To Be Published.
Page generated: Sat Aug 9 13:26:00 2025

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