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Potassium in PDB 5efh: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue, PDB code: 5efh was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.71 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.659, 92.414, 96.158, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.2

Other elements in 5efh:

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

Fluorine (F) 6 atoms
Zinc (Zn) 2 atoms
Bromine (Br) 7 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 Trifluoroketone Transition State Analogue (pdb code 5efh). 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue, PDB code: 5efh:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5efh

Go back to Potassium Binding Sites List in 5efh
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue


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 Trifluoroketone Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K2002

b:16.9
occ:1.00
O D:ASP612 2.6 10.2 1.0
O D:LEU634 2.7 13.2 1.0
O D:HIS614 2.7 12.8 1.0
OG D:SER633 2.7 12.2 1.0
OD1 D:ASP610 2.8 12.4 1.0
O D:ASP610 2.9 12.3 1.0
CG D:ASP610 3.3 12.8 1.0
C D:ASP610 3.5 11.6 1.0
C D:ASP612 3.6 13.6 1.0
C D:HIS614 3.6 13.5 1.0
C D:LEU634 3.7 13.7 1.0
CB D:ASP610 3.8 12.7 1.0
N D:ASP612 3.9 9.0 1.0
CB D:SER633 3.9 12.6 1.0
CB D:HIS635 4.0 13.1 1.0
N D:LEU634 4.0 13.0 1.0
OD2 D:ASP610 4.0 13.0 1.0
CA D:HIS615 4.1 13.8 1.0
CA D:ASP612 4.2 11.3 1.0
N D:TRP611 4.2 10.9 1.0
N D:HIS615 4.2 14.0 1.0
C D:TRP611 4.2 10.9 1.0
CB D:ASP612 4.3 10.8 1.0
CA D:ASP610 4.3 11.8 1.0
CA D:TRP611 4.3 10.8 1.0
ND1 D:HIS635 4.3 13.5 1.0
CA D:SER633 4.3 12.7 1.0
N D:GLY616 4.4 12.9 1.0
N D:HIS614 4.4 13.6 1.0
O D:HOH2143 4.5 9.1 1.0
CA D:HIS635 4.5 13.8 1.0
C D:SER633 4.5 13.2 1.0
N D:HIS635 4.5 14.0 1.0
CA D:LEU634 4.5 13.6 1.0
CG D:HIS635 4.6 14.9 1.0
C D:HIS615 4.6 13.6 1.0
C D:VAL613 4.7 14.2 1.0
N D:VAL613 4.7 12.7 1.0
CA D:HIS614 4.7 13.8 1.0
CE1 D:HIS573 4.7 11.7 1.0
OH D:TYR631 4.7 13.0 1.0
ND1 D:HIS573 4.9 13.2 1.0
CA D:VAL613 5.0 13.7 1.0
O D:TRP611 5.0 11.2 1.0

Potassium binding site 2 out of 4 in 5efh

Go back to Potassium Binding Sites List in 5efh
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue


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 Trifluoroketone Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K2003

b:19.0
occ:1.00
O D:VAL629 2.7 18.8 1.0
O D:PHE623 2.7 20.4 1.0
O D:TYR662 2.8 19.5 1.0
O D:HOH2118 2.8 25.5 1.0
O D:ASP626 2.9 24.1 1.0
O D:HOH2181 3.0 17.5 1.0
C D:TYR662 3.6 20.6 1.0
CB D:TYR662 3.6 22.5 1.0
C D:PHE623 3.7 20.2 1.0
CB D:PHE623 3.8 15.8 1.0
C D:VAL629 3.9 18.2 1.0
C D:ASP626 4.0 25.1 1.0
CA D:TYR662 4.2 21.9 1.0
N D:TYR631 4.3 14.9 1.0
CA D:PHE623 4.4 16.9 1.0
N D:ASN663 4.4 20.6 1.0
N D:ASP626 4.4 25.2 1.0
CB D:ASP626 4.4 24.8 1.0
CA D:ASP626 4.5 25.4 1.0
N D:GLU624 4.5 21.2 1.0
CA D:LEU630 4.6 16.4 1.0
CA D:GLU624 4.6 22.6 1.0
N D:LEU630 4.7 17.0 1.0
O D:GLY659 4.7 23.5 1.0
C D:GLU624 4.7 23.6 1.0
O D:GLU624 4.7 23.9 1.0
CB D:ASN663 4.7 19.8 1.0
CA D:ASN663 4.8 19.2 1.0
CB D:TYR631 4.8 14.1 1.0
CG D:TYR662 4.9 24.4 1.0
C D:LEU630 4.9 15.2 1.0
CA D:VAL629 4.9 18.8 1.0

Potassium binding site 3 out of 4 in 5efh

Go back to Potassium Binding Sites List in 5efh
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue


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 Trifluoroketone Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2002

b:18.4
occ:1.00
O A:ASP612 2.6 13.3 1.0
O A:LEU634 2.6 15.3 1.0
OG A:SER633 2.7 14.8 1.0
O A:HIS614 2.7 13.3 1.0
O A:ASP610 2.9 13.7 1.0
OD1 A:ASP610 2.9 11.7 1.0
CG A:ASP610 3.4 11.9 1.0
C A:ASP610 3.5 12.8 1.0
C A:LEU634 3.6 16.5 1.0
C A:ASP612 3.6 13.8 1.0
C A:HIS614 3.7 14.5 1.0
CB A:ASP610 3.7 12.4 1.0
N A:ASP612 3.8 11.9 1.0
N A:LEU634 3.9 16.2 1.0
CB A:HIS635 3.9 16.7 1.0
CB A:SER633 3.9 15.3 1.0
CA A:ASP612 4.1 11.8 1.0
N A:TRP611 4.2 12.5 1.0
OD2 A:ASP610 4.2 11.8 1.0
C A:TRP611 4.2 12.6 1.0
CA A:HIS615 4.2 14.8 1.0
CA A:ASP610 4.2 12.5 1.0
CB A:ASP612 4.3 11.2 1.0
CA A:SER633 4.3 15.7 1.0
CA A:TRP611 4.3 13.0 1.0
N A:HIS615 4.3 14.9 1.0
ND1 A:HIS635 4.3 17.4 1.0
C A:SER633 4.4 16.7 1.0
CA A:HIS635 4.4 17.3 1.0
N A:HIS635 4.4 17.8 1.0
CA A:LEU634 4.4 17.2 1.0
N A:HIS614 4.5 13.9 1.0
N A:GLY616 4.5 13.4 1.0
O A:HOH2117 4.5 14.5 1.0
CG A:HIS635 4.6 17.6 1.0
C A:VAL613 4.7 14.7 1.0
C A:HIS615 4.7 13.9 1.0
N A:VAL613 4.7 14.2 1.0
CA A:HIS614 4.7 14.9 1.0
OH A:TYR631 4.8 13.9 1.0
CE1 A:HIS573 4.9 9.5 1.0
O A:TRP611 5.0 13.1 1.0

Potassium binding site 4 out of 4 in 5efh

Go back to Potassium Binding Sites List in 5efh
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue


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 Trifluoroketone Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2003

b:22.0
occ:1.00
O A:VAL629 2.7 18.6 1.0
O A:PHE623 2.7 21.3 1.0
O A:TYR662 2.7 23.9 1.0
O A:HOH2185 2.8 12.2 1.0
O A:HOH2104 2.8 18.4 1.0
O A:ASP626 3.0 21.9 1.0
C A:TYR662 3.6 27.1 1.0
CB A:TYR662 3.6 28.4 1.0
C A:PHE623 3.7 20.0 1.0
CB A:PHE623 3.8 16.7 1.0
C A:VAL629 3.9 19.7 1.0
C A:ASP626 4.1 25.8 1.0
CA A:TYR662 4.2 25.6 1.0
N A:TYR631 4.3 18.1 1.0
CA A:PHE623 4.4 18.1 1.0
N A:ASN663 4.4 27.1 1.0
N A:GLU624 4.5 20.7 1.0
N A:ASP626 4.5 24.6 1.0
CA A:LEU630 4.5 20.1 1.0
CA A:GLU624 4.6 22.9 1.0
CB A:ASP626 4.6 23.8 1.0
CB A:TYR631 4.6 16.0 1.0
CA A:ASP626 4.7 24.9 1.0
N A:LEU630 4.7 19.8 1.0
O A:GLU624 4.7 22.6 1.0
C A:GLU624 4.7 24.3 1.0
O A:GLY659 4.7 25.9 1.0
CB A:ASN663 4.7 23.7 1.0
CA A:ASN663 4.8 26.4 1.0
C A:LEU630 4.8 18.4 1.0
CG A:TYR662 4.9 29.7 1.0
CA A:VAL629 4.9 19.5 1.0
OD1 A:ASN663 5.0 25.3 1.0

Reference:

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134
Page generated: Sun Dec 13 23:56:58 2020

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