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Potassium in PDB 6thv: X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A

Protein crystallography data

The structure of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A, PDB code: 6thv was solved by C.Barinka, L.Motlova, M.Svoboda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.90 / 1.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.278, 93.713, 51.574, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 16.9

Other elements in 6thv:

The structure of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A (pdb code 6thv). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A, PDB code: 6thv:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 6thv

Go back to Potassium Binding Sites List in 6thv
Potassium binding site 1 out of 3 in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:6.7
occ:1.00
O A:ASP612 2.6 7.0 1.0
O A:LEU634 2.7 6.9 1.0
O A:HIS614 2.7 6.9 1.0
OD1 A:ASP610 2.7 7.3 1.0
OG A:SER633 2.7 7.2 1.0
O A:ASP610 2.8 6.9 1.0
CG A:ASP610 3.3 7.0 1.0
C A:ASP610 3.5 6.5 1.0
C A:ASP612 3.6 6.8 1.0
C A:HIS614 3.7 6.6 1.0
C A:LEU634 3.7 6.4 1.0
N A:ASP612 3.8 7.1 1.0
CB A:ASP610 3.9 7.2 1.0
N A:LEU634 3.9 6.8 1.0
OD2 A:ASP610 3.9 8.2 1.0
CB A:SER633 4.0 7.5 1.0
CB A:HIS635 4.0 7.1 1.0
CA A:ASP612 4.2 6.8 1.0
N A:TRP611 4.2 6.8 1.0
C A:TRP611 4.2 6.6 1.0
CB A:ASP612 4.3 7.4 1.0
CA A:ASP610 4.3 6.8 1.0
CA A:SER633 4.3 6.9 1.0
CA A:HIS615 4.3 6.9 1.0
ND1 A:HIS635 4.3 7.2 1.0
CA A:TRP611 4.4 6.9 1.0
N A:HIS615 4.4 7.0 1.0
N A:HIS614 4.4 7.0 1.0
N A:GLY616 4.5 7.0 1.0
C A:SER633 4.5 6.8 1.0
CA A:HIS635 4.5 6.7 1.0
CA A:LEU634 4.5 6.8 1.0
O A:HOH917 4.5 8.8 1.0
N A:HIS635 4.6 6.4 1.0
CG A:HIS635 4.7 7.1 1.0
C A:VAL613 4.7 6.7 1.0
OH A:TYR631 4.7 7.8 1.0
CA A:HIS614 4.7 6.8 1.0
N A:VAL613 4.7 6.8 1.0
CE1 A:HIS573 4.7 8.8 1.0
C A:HIS615 4.7 7.0 1.0
ND1 A:HIS573 4.9 8.2 1.0
O A:TRP611 4.9 7.2 1.0

Potassium binding site 2 out of 3 in 6thv

Go back to Potassium Binding Sites List in 6thv
Potassium binding site 2 out of 3 in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:8.0
occ:1.00
O A:VAL629 2.6 9.2 1.0
O A:HOH985 2.7 8.9 1.0
O A:PHE623 2.7 8.3 1.0
O A:TYR662 2.8 7.3 1.0
O A:ASP626 2.9 9.3 0.5
O A:HOH1030 2.9 8.6 1.0
O A:ASP626 3.0 10.1 0.5
C A:TYR662 3.6 6.9 1.0
C A:PHE623 3.6 8.1 1.0
CB A:TYR662 3.7 8.1 1.0
CB A:PHE623 3.7 8.1 1.0
C A:VAL629 3.9 7.7 1.0
C A:ASP626 4.0 10.2 0.5
C A:ASP626 4.1 10.2 0.5
CA A:TYR662 4.2 7.5 1.0
CA A:PHE623 4.3 8.2 1.0
N A:TYR631 4.3 6.9 1.0
N A:ASN663 4.4 7.0 1.0
N A:ASP626 4.4 10.8 0.5
CB A:ASP626 4.4 11.4 0.5
N A:ASP626 4.5 10.4 0.5
N A:GLU624 4.6 8.6 1.0
CA A:ASP626 4.6 10.3 0.5
CA A:LEU630 4.6 7.3 1.0
CB A:ASP626 4.6 14.3 0.5
CA A:ASP626 4.6 11.5 0.5
CA A:GLU624 4.6 8.9 1.0
N A:LEU630 4.7 7.5 1.0
O A:GLU624 4.7 9.5 1.0
C A:GLU624 4.7 9.0 1.0
CB A:TYR631 4.8 7.6 1.0
CA A:ASN663 4.8 7.0 1.0
CB A:ASN663 4.8 7.6 1.0
O A:GLY659 4.9 10.2 1.0
CA A:VAL629 4.9 8.3 1.0
C A:LEU630 4.9 6.8 1.0
OD1 A:ASN663 5.0 7.7 1.0
CG A:PHE623 5.0 8.0 1.0

Potassium binding site 3 out of 3 in 6thv

Go back to Potassium Binding Sites List in 6thv
Potassium binding site 3 out of 3 in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K811

b:35.5
occ:0.40
O A:HOH948 2.4 26.6 1.0
O A:HOH984 2.5 28.9 1.0
O A:HOH1245 2.7 19.7 1.0
O A:HOH946 3.9 15.2 1.0
O A:HOH1197 4.1 29.6 1.0
CA A:ALA789 4.2 8.8 1.0
CB A:ALA789 4.2 9.2 1.0
O A:ALA789 4.4 8.7 1.0
O A:HOH1253 4.4 29.9 1.0
CG1 A:VAL654 4.6 9.3 1.0
O A:ASP652 4.6 10.9 1.0
CB A:ASP652 4.6 12.3 1.0
CA A:ASP652 4.6 9.6 1.0
C A:ALA789 4.8 8.1 1.0
NH2 A:ARG660 4.9 15.3 1.0
O A:HOH971 4.9 17.3 1.0

Reference:

C.Barinka, L.Motlova, M.Svoboda. X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor Tubastatin A To Be Published.
Page generated: Mon Dec 14 01:38:22 2020

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