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Potassium in PDB 5thv: Crystal Structure of G305A HDAC8 in Complex with M344

Enzymatic activity of Crystal Structure of G305A HDAC8 in Complex with M344

All present enzymatic activity of Crystal Structure of G305A HDAC8 in Complex with M344:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of G305A HDAC8 in Complex with M344, PDB code: 5thv 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) 52.37 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.030, 82.952, 94.550, 90.00, 99.05, 90.00
R / Rfree (%) 17.2 / 21

Other elements in 5thv:

The structure of Crystal Structure of G305A HDAC8 in Complex with M344 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of G305A HDAC8 in Complex with M344 (pdb code 5thv). 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 G305A HDAC8 in Complex with M344, PDB code: 5thv:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5thv

Go back to Potassium Binding Sites List in 5thv
Potassium binding site 1 out of 4 in the Crystal Structure of G305A HDAC8 in Complex with M344


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 G305A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:16.6
occ:1.00
O A:LEU200 2.6 16.6 1.0
O A:ASP178 2.6 16.2 1.0
OD1 A:ASP176 2.7 13.5 1.0
O A:HIS180 2.8 15.2 1.0
O A:ASP176 2.8 14.3 1.0
OG A:SER199 2.9 17.1 1.0
C A:ASP176 3.4 15.5 1.0
CG A:ASP176 3.4 15.5 1.0
N A:ASP178 3.5 17.0 1.0
C A:ASP178 3.5 16.5 1.0
C A:LEU200 3.6 17.4 1.0
C A:HIS180 3.7 15.4 1.0
CB A:HIS201 3.7 14.9 1.0
CB A:ASP176 3.8 14.2 1.0
CA A:ASP178 3.9 17.7 1.0
CB A:ASP178 3.9 18.2 1.0
N A:LEU200 3.9 18.1 1.0
C A:LEU177 4.0 14.7 1.0
N A:LEU177 4.0 16.4 1.0
CB A:SER199 4.1 14.0 1.0
CA A:LEU177 4.2 17.5 1.0
CA A:ASP176 4.2 16.5 1.0
CA A:HIS201 4.3 15.2 1.0
ND1 A:HIS201 4.3 15.4 1.0
OD2 A:ASP176 4.3 17.8 1.0
N A:GLY182 4.3 16.6 1.0
CA A:SER199 4.3 17.6 1.0
N A:HIS201 4.3 16.1 1.0
CA A:HIS181 4.4 15.1 1.0
N A:HIS181 4.4 15.4 1.0
CA A:LEU200 4.4 16.5 1.0
O A:HOH533 4.5 18.0 1.0
C A:SER199 4.5 20.0 1.0
N A:HIS180 4.5 15.0 1.0
CG A:HIS201 4.5 15.6 1.0
C A:HIS181 4.7 18.0 1.0
C A:LEU179 4.7 19.9 1.0
N A:LEU179 4.7 16.0 1.0
CA A:HIS180 4.7 16.7 1.0
O A:LEU177 4.8 18.6 1.0
CE1 A:HIS142 4.9 19.4 1.0

Potassium binding site 2 out of 4 in 5thv

Go back to Potassium Binding Sites List in 5thv
Potassium binding site 2 out of 4 in the Crystal Structure of G305A HDAC8 in Complex with M344


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 G305A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:23.6
occ:1.00
O A:PHE189 2.5 26.0 1.0
O A:VAL195 2.6 23.1 1.0
O A:THR192 2.8 25.5 1.0
O A:HOH630 2.8 17.8 1.0
O A:HOH519 2.8 27.1 1.0
O A:TYR225 3.0 21.7 1.0
C A:PHE189 3.5 21.6 1.0
CB A:TYR225 3.6 25.4 1.0
C A:TYR225 3.7 23.4 1.0
C A:VAL195 3.8 16.5 1.0
CB A:PHE189 4.0 21.1 1.0
C A:THR192 4.0 29.2 1.0
OG A:SER226 4.2 24.1 1.0
CA A:TYR225 4.3 23.1 1.0
CA A:SER190 4.3 23.8 0.4
N A:SER190 4.3 20.8 0.4
CA A:SER190 4.3 23.8 0.6
N A:SER190 4.3 20.7 0.6
CA A:PHE189 4.4 23.8 1.0
CA A:MET196 4.4 22.8 1.0
O A:SER190 4.4 24.4 0.6
CG2 A:THR192 4.4 23.2 1.0
C A:SER190 4.5 23.5 0.6
N A:SER226 4.5 19.9 1.0
N A:THR192 4.5 25.5 1.0
C A:SER190 4.5 23.6 0.4
N A:MET196 4.6 21.6 1.0
O A:GLY222 4.6 25.5 1.0
N A:THR197 4.7 20.1 1.0
O A:SER190 4.7 24.5 0.4
CA A:THR192 4.8 24.4 1.0
CA A:VAL195 4.8 19.4 1.0
CG A:TYR225 4.9 26.0 1.0
CA A:GLY222 4.9 27.2 1.0
N A:VAL195 5.0 24.2 1.0
OG1 A:THR197 5.0 22.1 1.0
N A:SER193 5.0 25.6 1.0

Potassium binding site 3 out of 4 in 5thv

Go back to Potassium Binding Sites List in 5thv
Potassium binding site 3 out of 4 in the Crystal Structure of G305A HDAC8 in Complex with M344


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 G305A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:16.3
occ:1.00
O B:LEU200 2.6 19.2 1.0
OD1 B:ASP176 2.7 14.4 1.0
O B:ASP178 2.7 15.6 1.0
O B:ASP176 2.7 16.7 1.0
O B:HIS180 2.8 15.9 1.0
OG B:SER199 2.8 18.6 1.0
C B:ASP176 3.4 15.9 1.0
CG B:ASP176 3.4 20.4 1.0
N B:ASP178 3.5 16.0 1.0
C B:ASP178 3.5 16.9 1.0
C B:LEU200 3.6 17.7 1.0
C B:HIS180 3.8 13.6 1.0
CB B:HIS201 3.8 15.2 1.0
CB B:ASP176 3.8 17.5 1.0
CA B:ASP178 3.9 16.5 1.0
CB B:ASP178 3.9 17.5 1.0
C B:LEU177 4.0 16.2 1.0
N B:LEU200 4.0 19.5 1.0
N B:LEU177 4.0 15.3 1.0
CB B:SER199 4.1 16.5 1.0
CA B:LEU177 4.2 16.7 1.0
CA B:ASP176 4.2 17.3 1.0
CA B:HIS201 4.3 16.9 1.0
ND1 B:HIS201 4.3 18.7 1.0
N B:GLY182 4.3 16.4 1.0
OD2 B:ASP176 4.3 17.7 1.0
CA B:SER199 4.4 17.6 1.0
N B:HIS201 4.4 19.2 1.0
CA B:HIS181 4.4 16.3 1.0
N B:HIS180 4.4 14.0 1.0
CA B:LEU200 4.5 16.7 1.0
N B:HIS181 4.5 13.3 1.0
C B:SER199 4.5 16.9 1.0
O B:HOH550 4.5 17.0 1.0
CG B:HIS201 4.5 17.3 1.0
C B:LEU179 4.7 14.3 1.0
C B:HIS181 4.7 17.2 1.0
N B:LEU179 4.7 14.9 1.0
CA B:HIS180 4.7 15.1 1.0
O B:LEU177 4.8 16.6 1.0
CE1 B:HIS142 4.9 19.6 1.0
O B:LEU179 5.0 13.9 1.0

Potassium binding site 4 out of 4 in 5thv

Go back to Potassium Binding Sites List in 5thv
Potassium binding site 4 out of 4 in the Crystal Structure of G305A HDAC8 in Complex with M344


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 G305A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:22.7
occ:1.00
O B:VAL195 2.6 26.8 1.0
O B:PHE189 2.6 23.1 1.0
O B:HOH631 2.8 18.6 1.0
O B:THR192 2.8 25.1 1.0
O B:HOH534 2.9 24.2 1.0
O B:TYR225 3.0 20.9 1.0
C B:PHE189 3.6 19.7 1.0
CB B:TYR225 3.6 25.0 1.0
C B:TYR225 3.7 27.1 1.0
C B:VAL195 3.8 20.2 1.0
C B:THR192 4.0 31.0 1.0
CB B:PHE189 4.0 19.2 1.0
OG B:SER226 4.2 21.9 1.0
CA B:TYR225 4.3 24.5 1.0
CG2 B:THR192 4.3 27.0 1.0
CA B:SER190 4.3 23.0 0.5
N B:SER190 4.4 20.2 0.5
CA B:SER190 4.4 23.0 0.5
N B:SER190 4.4 20.1 0.5
CA B:PHE189 4.4 23.1 1.0
CA B:MET196 4.4 24.5 1.0
N B:SER226 4.5 25.1 1.0
C B:SER190 4.5 25.2 0.5
O B:SER190 4.5 25.0 0.5
C B:SER190 4.5 25.2 0.5
N B:THR192 4.5 25.7 1.0
N B:MET196 4.6 22.7 1.0
O B:GLY222 4.6 27.9 1.0
O B:SER190 4.7 24.9 0.5
N B:THR197 4.7 21.8 1.0
CA B:THR192 4.8 24.4 1.0
CA B:VAL195 4.8 19.9 1.0
CA B:GLY222 4.9 27.9 1.0
CG B:TYR225 4.9 24.6 1.0
N B:VAL195 4.9 22.7 1.0
CG2 B:THR197 5.0 22.6 1.0
CB B:VAL195 5.0 21.4 1.0
N B:SER193 5.0 23.5 1.0

Reference:

N.J.Porter, N.H.Christianson, C.Decroos, D.W.Christianson. Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8. Biochemistry V. 55 6718 2016.
ISSN: ISSN 1520-4995
PubMed: 27933794
DOI: 10.1021/ACS.BIOCHEM.6B01014
Page generated: Mon Dec 14 00:07:53 2020

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