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Potassium in PDB 8qa7: Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.

Protein crystallography data

The structure of Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component., PDB code: 8qa7 was solved by J.Sandmark, M.Ek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.63 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.39, 92.373, 96.19, 90, 90, 90
R / Rfree (%) 21.7 / 24

Other elements in 8qa7:

The structure of Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. (pdb code 8qa7). 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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component., PDB code: 8qa7:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8qa7

Go back to Potassium Binding Sites List in 8qa7
Potassium binding site 1 out of 4 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.


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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K801

b:21.1
occ:1.00
O A:ASP612 2.6 16.2 1.0
OD1 A:ASP610 2.7 16.0 1.0
O A:HIS614 2.8 16.3 1.0
O A:LEU634 2.8 18.4 1.0
OG A:SER633 2.8 17.8 1.0
O A:ASP610 2.8 16.6 1.0
CG A:ASP610 3.3 16.9 1.0
C A:ASP610 3.5 16.7 1.0
C A:ASP612 3.7 16.1 1.0
C A:HIS614 3.7 16.6 1.0
C A:LEU634 3.8 18.4 1.0
N A:ASP612 3.9 16.9 1.0
CB A:ASP610 3.9 16.4 1.0
OD2 A:ASP610 4.0 17.1 1.0
N A:LEU634 4.0 17.8 1.0
CB A:SER633 4.0 17.0 1.0
CB A:HIS635 4.1 17.8 1.0
CA A:ASP612 4.2 16.2 1.0
N A:TRP611 4.2 16.0 1.0
C A:TRP611 4.2 16.4 1.0
CA A:HIS615 4.3 16.4 1.0
CA A:ASP610 4.3 16.1 1.0
CB A:ASP612 4.3 16.5 1.0
CA A:SER633 4.3 17.6 1.0
CA A:TRP611 4.3 16.5 1.0
ND1 A:HIS635 4.4 18.5 1.0
N A:HIS615 4.4 15.9 1.0
N A:GLY616 4.4 16.2 1.0
C A:SER633 4.5 17.9 1.0
N A:HIS614 4.5 16.4 1.0
CA A:HIS635 4.5 17.5 1.0
CA A:LEU634 4.6 18.8 1.0
N A:HIS635 4.6 17.6 1.0
CG A:HIS635 4.7 18.5 1.0
O A:HOH909 4.7 18.7 1.0
C A:HIS615 4.7 16.1 1.0
C A:VAL613 4.7 16.6 1.0
CE1 A:HIS573 4.7 16.6 1.0
N A:VAL613 4.7 15.7 1.0
CA A:HIS614 4.7 16.1 1.0
OH A:TYR631 4.8 18.4 1.0
ND1 A:HIS573 4.9 16.4 1.0
O A:TRP611 5.0 17.3 1.0

Potassium binding site 2 out of 4 in 8qa7

Go back to Potassium Binding Sites List in 8qa7
Potassium binding site 2 out of 4 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.


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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:43.0
occ:1.00
O A:HOH920 2.7 23.0 1.0
O A:PHE623 2.9 20.2 1.0
O A:TYR662 2.9 22.6 1.0
O A:HOH931 2.9 21.7 1.0
O A:VAL629 2.9 22.6 1.0
O A:ASP626 3.2 27.1 1.0
C A:TYR662 3.6 22.0 1.0
C A:PHE623 3.7 20.5 1.0
CB A:PHE623 3.8 20.3 1.0
CB A:TYR662 3.9 23.8 1.0
C A:VAL629 4.1 21.1 1.0
N A:ASN663 4.2 21.6 1.0
N A:TYR631 4.3 17.8 1.0
CA A:TYR662 4.3 23.2 1.0
C A:ASP626 4.3 27.2 1.0
CA A:PHE623 4.4 19.9 1.0
N A:GLU624 4.5 21.8 1.0
CB A:TYR631 4.5 17.4 1.0
CA A:ASN663 4.5 21.4 1.0
CA A:GLU624 4.5 24.8 1.0
CB A:ASN663 4.6 21.3 1.0
CA A:LEU630 4.7 19.7 1.0
O A:GLU624 4.7 23.0 1.0
OD1 A:ASN663 4.7 21.3 1.0
N A:ASP626 4.7 25.2 1.0
C A:GLU624 4.7 24.4 1.0
O A:GLY659 4.9 26.3 1.0
N A:LEU630 4.9 20.2 1.0
C A:LEU630 4.9 18.7 1.0
CA A:ASP626 4.9 25.9 1.0
CB A:ASP626 4.9 27.6 1.0

Potassium binding site 3 out of 4 in 8qa7

Go back to Potassium Binding Sites List in 8qa7
Potassium binding site 3 out of 4 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.


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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K801

b:24.0
occ:1.00
O B:ASP612 2.6 18.8 1.0
O B:LEU634 2.7 19.7 1.0
OD1 B:ASP610 2.8 17.9 1.0
O B:HIS614 2.8 18.9 1.0
O B:ASP610 2.8 18.4 1.0
OG B:SER633 2.9 19.2 1.0
CG B:ASP610 3.3 18.6 1.0
C B:ASP610 3.5 18.6 1.0
C B:ASP612 3.6 18.4 1.0
C B:HIS614 3.7 18.4 1.0
C B:LEU634 3.7 19.8 1.0
CB B:ASP610 3.8 18.5 1.0
N B:ASP612 3.9 18.0 1.0
N B:LEU634 4.0 18.8 1.0
OD2 B:ASP610 4.0 18.7 1.0
CB B:SER633 4.0 19.1 1.0
CB B:HIS635 4.1 20.2 1.0
CA B:ASP612 4.2 17.6 1.0
N B:TRP611 4.2 18.1 1.0
CA B:HIS615 4.2 17.6 1.0
CA B:ASP610 4.3 18.4 1.0
C B:TRP611 4.3 18.5 1.0
CB B:ASP612 4.3 18.3 1.0
CA B:SER633 4.3 19.2 1.0
N B:HIS615 4.3 17.8 1.0
ND1 B:HIS635 4.4 20.4 1.0
CA B:TRP611 4.4 18.5 1.0
N B:GLY616 4.4 17.6 1.0
C B:SER633 4.5 20.2 1.0
CA B:HIS635 4.5 19.8 1.0
N B:HIS614 4.5 18.7 1.0
N B:HIS635 4.5 19.6 1.0
CA B:LEU634 4.5 20.1 1.0
O B:HOH904 4.6 24.1 1.0
CG B:HIS635 4.7 20.1 1.0
C B:HIS615 4.7 17.5 1.0
C B:VAL613 4.7 19.3 1.0
N B:VAL613 4.7 18.6 1.0
OH B:TYR631 4.8 18.1 1.0
CA B:HIS614 4.8 19.0 1.0
CE1 B:HIS573 4.8 17.4 1.0
ND1 B:HIS573 4.9 17.3 1.0
O B:TRP611 5.0 19.8 1.0

Potassium binding site 4 out of 4 in 8qa7

Go back to Potassium Binding Sites List in 8qa7
Potassium binding site 4 out of 4 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.


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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:41.6
occ:1.00
O B:HOH909 2.8 23.0 1.0
O B:VAL629 2.8 22.9 1.0
O B:PHE623 2.8 20.5 1.0
O B:HOH962 2.9 21.1 1.0
O B:TYR662 2.9 23.4 1.0
O B:ASP626 3.1 27.3 1.0
C B:TYR662 3.7 23.9 1.0
C B:PHE623 3.7 20.4 1.0
CB B:PHE623 3.8 20.3 1.0
CB B:TYR662 3.9 25.0 1.0
C B:VAL629 4.0 21.6 1.0
C B:ASP626 4.3 26.7 1.0
N B:TYR631 4.3 19.4 1.0
N B:ASN663 4.3 22.0 1.0
CA B:PHE623 4.4 20.2 1.0
CA B:TYR662 4.4 24.2 1.0
N B:GLU624 4.5 22.0 1.0
CB B:TYR631 4.6 18.4 1.0
CA B:GLU624 4.6 23.1 1.0
CA B:LEU630 4.6 21.1 1.0
CA B:ASN663 4.7 22.4 1.0
CB B:ASN663 4.7 22.0 1.0
N B:ASP626 4.7 25.2 1.0
O B:GLU624 4.7 21.7 1.0
C B:GLU624 4.8 23.3 1.0
N B:LEU630 4.8 20.6 1.0
OD1 B:ASN663 4.8 22.2 1.0
CA B:ASP626 4.9 26.5 1.0
C B:LEU630 4.9 20.5 1.0
O B:GLY659 4.9 27.6 1.0
CB B:ASP626 4.9 28.8 1.0

Reference:

J.Sandmark, M.Ek. Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. To Be Published.
Page generated: Sat Sep 28 22:14:29 2024

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