Atomistry » Potassium » PDB 5sc8-5u3q » 5tht
Atomistry »
  Potassium »
    PDB 5sc8-5u3q »
      5tht »

Potassium in PDB 5tht: Crystal Structure of G303A HDAC8 in Complex with M344

Enzymatic activity of Crystal Structure of G303A HDAC8 in Complex with M344

All present enzymatic activity of Crystal Structure of G303A HDAC8 in Complex with M344:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of G303A HDAC8 in Complex with M344, PDB code: 5tht 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) 97.66 / 2.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.700, 83.810, 99.780, 90.00, 91.72, 90.00
R / Rfree (%) 18 / 21.2

Other elements in 5tht:

The structure of Crystal Structure of G303A HDAC8 in Complex with M344 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of G303A HDAC8 in Complex with M344 (pdb code 5tht). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of G303A HDAC8 in Complex with M344, PDB code: 5tht:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5tht

Go back to Potassium Binding Sites List in 5tht
Potassium binding site 1 out of 8 in the Crystal Structure of G303A 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 G303A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:16.4
occ:1.00
O A:ASP178 2.7 13.1 1.0
O A:HIS180 2.7 11.1 1.0
O A:LEU200 2.7 12.5 1.0
OD1 A:ASP176 2.8 16.4 1.0
O A:ASP176 2.9 13.8 1.0
OG A:SER199 2.9 13.4 1.0
CG A:ASP176 3.4 17.0 1.0
N A:ASP178 3.4 15.7 1.0
C A:ASP176 3.4 17.8 1.0
C A:ASP178 3.5 12.7 1.0
C A:LEU200 3.6 12.0 1.0
CB A:ASP176 3.7 16.7 1.0
CB A:HIS201 3.8 12.4 1.0
C A:HIS180 3.8 10.7 1.0
CA A:ASP178 3.8 12.8 1.0
N A:LEU200 3.9 12.7 1.0
C A:LEU177 4.0 13.6 1.0
CB A:ASP178 4.0 11.5 1.0
N A:LEU177 4.1 15.5 1.0
CB A:SER199 4.1 16.7 1.0
CA A:ASP176 4.2 14.7 1.0
OD2 A:ASP176 4.2 17.7 1.0
CA A:LEU177 4.2 15.0 1.0
ND1 A:HIS201 4.3 14.3 1.0
CA A:HIS201 4.3 13.7 1.0
CA A:SER199 4.3 16.2 1.0
N A:HIS201 4.4 10.1 1.0
C A:SER199 4.4 13.8 1.0
N A:GLY182 4.4 12.5 1.0
CA A:LEU200 4.4 13.4 1.0
O A:HOH503 4.5 13.1 1.0
CA A:HIS181 4.5 12.8 1.0
N A:HIS180 4.5 11.5 1.0
CG A:HIS201 4.5 13.0 1.0
N A:HIS181 4.5 11.6 1.0
N A:LEU179 4.6 18.2 1.0
C A:LEU179 4.7 13.0 1.0
O A:LEU177 4.7 14.6 1.0
CA A:HIS180 4.8 14.5 1.0
C A:HIS181 4.8 13.3 1.0
CE1 A:HIS142 4.9 16.5 1.0
O A:LEU179 5.0 11.9 1.0

Potassium binding site 2 out of 8 in 5tht

Go back to Potassium Binding Sites List in 5tht
Potassium binding site 2 out of 8 in the Crystal Structure of G303A 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 G303A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:17.7
occ:1.00
O A:PHE189 2.6 18.4 1.0
O A:VAL195 2.6 19.5 1.0
O A:HOH505 2.8 15.8 1.0
O A:THR192 2.9 25.4 1.0
O A:HOH543 3.0 15.1 1.0
O A:TYR225 3.0 17.6 1.0
C A:PHE189 3.6 18.0 1.0
CB A:TYR225 3.6 17.2 1.0
C A:TYR225 3.7 19.2 1.0
C A:VAL195 3.9 18.5 1.0
OG A:SER226 4.0 21.2 1.0
CB A:PHE189 4.1 13.1 1.0
C A:THR192 4.1 25.0 1.0
CA A:TYR225 4.3 21.6 1.0
CA A:SER190 4.3 18.3 1.0
O A:GLY222 4.4 21.1 1.0
CA A:MET196 4.4 15.7 1.0
N A:SER190 4.4 16.5 1.0
CG2 A:THR192 4.5 17.9 1.0
CA A:PHE189 4.5 19.5 1.0
N A:SER226 4.5 15.4 1.0
N A:MET196 4.6 16.3 1.0
N A:THR192 4.6 22.5 1.0
C A:SER190 4.6 19.6 1.0
N A:THR197 4.6 15.9 1.0
OG1 A:THR197 4.7 22.7 1.0
O A:SER190 4.8 23.9 1.0
CA A:GLY222 4.8 20.0 1.0
CA A:THR192 4.9 23.1 1.0
CG A:TYR225 4.9 19.9 1.0
CA A:VAL195 4.9 18.4 1.0
CA A:SER226 5.0 20.6 1.0
C A:MET196 5.0 19.7 1.0

Potassium binding site 3 out of 8 in 5tht

Go back to Potassium Binding Sites List in 5tht
Potassium binding site 3 out of 8 in the Crystal Structure of G303A 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 G303A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:17.1
occ:1.00
O B:ASP178 2.7 11.8 1.0
O B:LEU200 2.7 12.6 1.0
O B:HIS180 2.8 14.0 1.0
OD1 B:ASP176 2.8 18.1 1.0
O B:ASP176 2.8 14.1 1.0
OG B:SER199 3.0 16.1 1.0
CG B:ASP176 3.3 16.9 1.0
C B:ASP176 3.4 16.2 1.0
N B:ASP178 3.4 16.9 1.0
C B:ASP178 3.5 13.1 1.0
C B:LEU200 3.6 14.8 1.0
CB B:ASP176 3.6 19.6 1.0
C B:HIS180 3.8 14.3 1.0
CB B:HIS201 3.8 12.7 1.0
CA B:ASP178 3.8 13.3 1.0
N B:LEU200 3.9 15.3 1.0
C B:LEU177 3.9 16.9 1.0
N B:LEU177 3.9 15.4 1.0
CB B:ASP178 4.0 12.7 1.0
CB B:SER199 4.1 16.9 1.0
CA B:ASP176 4.1 17.5 1.0
CA B:LEU177 4.1 19.3 1.0
OD2 B:ASP176 4.2 20.2 1.0
ND1 B:HIS201 4.3 15.7 1.0
CA B:HIS201 4.3 11.6 1.0
CA B:SER199 4.3 17.1 1.0
N B:HIS201 4.3 12.0 1.0
C B:SER199 4.4 16.3 1.0
CA B:LEU200 4.4 14.7 1.0
N B:GLY182 4.4 14.1 1.0
CA B:HIS181 4.5 15.5 1.0
N B:HIS180 4.5 9.5 1.0
N B:HIS181 4.5 12.3 1.0
CG B:HIS201 4.5 15.8 1.0
O B:HOH503 4.6 10.3 1.0
N B:LEU179 4.7 16.8 1.0
O B:LEU177 4.7 16.3 1.0
C B:LEU179 4.7 15.2 1.0
CA B:HIS180 4.8 13.6 1.0
C B:HIS181 4.8 14.5 1.0
CE1 B:HIS142 4.9 15.6 1.0

Potassium binding site 4 out of 8 in 5tht

Go back to Potassium Binding Sites List in 5tht
Potassium binding site 4 out of 8 in the Crystal Structure of G303A 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 G303A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:17.7
occ:1.00
O B:PHE189 2.6 17.4 1.0
O B:VAL195 2.7 20.2 1.0
O B:HOH506 2.8 17.6 1.0
O B:HOH537 3.0 13.9 1.0
O B:TYR225 3.0 19.2 1.0
O B:THR192 3.0 24.1 1.0
C B:PHE189 3.6 15.8 1.0
C B:TYR225 3.7 21.7 1.0
CB B:TYR225 3.7 19.4 1.0
OG B:SER226 3.8 24.7 1.0
C B:VAL195 3.9 20.9 1.0
CB B:PHE189 4.0 15.4 1.0
C B:THR192 4.2 26.1 1.0
CA B:SER190 4.3 18.4 1.0
N B:SER190 4.3 14.4 1.0
CA B:TYR225 4.4 21.6 1.0
CA B:MET196 4.4 21.8 1.0
CA B:PHE189 4.5 15.7 1.0
CG2 B:THR192 4.5 17.8 1.0
O B:GLY222 4.5 24.4 1.0
N B:SER226 4.5 18.8 1.0
C B:SER190 4.6 22.7 1.0
N B:THR197 4.6 18.8 1.0
N B:MET196 4.6 22.8 1.0
N B:THR192 4.6 16.0 1.0
OG1 B:THR197 4.8 17.8 1.0
O B:SER190 4.8 23.1 1.0
CA B:SER226 4.9 19.9 1.0
CA B:GLY222 4.9 22.2 1.0
CA B:THR192 4.9 22.6 1.0
CB B:SER226 5.0 18.3 1.0
CA B:VAL195 5.0 22.0 1.0
C B:MET196 5.0 18.4 1.0

Potassium binding site 5 out of 8 in 5tht

Go back to Potassium Binding Sites List in 5tht
Potassium binding site 5 out of 8 in the Crystal Structure of G303A 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 5 of Crystal Structure of G303A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K403

b:18.1
occ:1.00
O C:ASP178 2.7 13.8 1.0
O C:HIS180 2.8 19.1 1.0
OD1 C:ASP176 2.8 15.2 1.0
O C:LEU200 2.9 23.0 1.0
O C:ASP176 2.9 14.3 1.0
OG C:SER199 2.9 17.5 1.0
CG C:ASP176 3.3 18.1 1.0
C C:ASP176 3.4 17.1 1.0
N C:ASP178 3.5 17.2 1.0
C C:ASP178 3.6 14.7 1.0
C C:LEU200 3.7 18.6 1.0
CB C:ASP176 3.7 12.3 1.0
CB C:HIS201 3.8 17.7 1.0
C C:HIS180 3.8 20.1 1.0
CA C:ASP178 3.9 15.1 1.0
N C:LEU200 4.0 22.0 1.0
CB C:SER199 4.0 15.5 1.0
C C:LEU177 4.0 17.2 1.0
CB C:ASP178 4.1 13.2 1.0
N C:LEU177 4.1 14.8 1.0
OD2 C:ASP176 4.1 22.1 1.0
CA C:ASP176 4.2 12.4 1.0
CA C:SER199 4.2 17.6 1.0
CA C:LEU177 4.3 15.7 1.0
CA C:HIS201 4.3 18.1 1.0
C C:SER199 4.3 23.0 1.0
N C:GLY182 4.3 21.6 1.0
N C:HIS201 4.4 19.0 1.0
CA C:HIS181 4.4 20.2 1.0
ND1 C:HIS201 4.4 17.3 1.0
CA C:LEU200 4.5 17.6 1.0
N C:HIS181 4.5 21.2 1.0
N C:HIS180 4.6 16.0 1.0
O C:HOH503 4.6 15.8 1.0
CG C:HIS201 4.6 18.9 1.0
N C:LEU179 4.7 14.4 1.0
C C:LEU179 4.7 16.6 1.0
CE1 C:HIS142 4.7 18.0 1.0
C C:HIS181 4.8 18.3 1.0
O C:LEU177 4.8 18.0 1.0
CA C:HIS180 4.8 16.0 1.0
O C:LEU179 5.0 17.4 1.0

Potassium binding site 6 out of 8 in 5tht

Go back to Potassium Binding Sites List in 5tht
Potassium binding site 6 out of 8 in the Crystal Structure of G303A 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 6 of Crystal Structure of G303A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K404

b:23.6
occ:1.00
O C:PHE189 2.6 22.4 1.0
O C:VAL195 2.7 17.3 1.0
O C:HOH502 2.8 22.3 1.0
O C:HOH528 2.9 21.1 1.0
O C:TYR225 3.0 22.4 1.0
O C:THR192 3.0 25.2 1.0
C C:PHE189 3.6 20.8 1.0
CB C:TYR225 3.7 24.2 1.0
C C:TYR225 3.7 26.5 1.0
OG C:SER226 3.7 29.7 1.0
C C:VAL195 3.9 21.8 1.0
CB C:PHE189 4.1 18.9 1.0
C C:THR192 4.2 25.5 1.0
CA C:SER190 4.3 21.3 1.0
CA C:TYR225 4.3 25.6 1.0
N C:SER190 4.3 17.7 1.0
O C:GLY222 4.4 28.2 1.0
CA C:MET196 4.4 19.0 1.0
N C:SER226 4.5 23.8 1.0
CA C:PHE189 4.5 19.3 1.0
C C:SER190 4.6 25.2 1.0
N C:MET196 4.6 21.5 1.0
CG2 C:THR192 4.6 18.0 1.0
O C:SER190 4.7 30.1 1.0
N C:THR197 4.7 18.1 1.0
N C:THR192 4.7 24.0 1.0
OG1 C:THR197 4.8 23.7 1.0
CB C:SER226 4.9 18.7 1.0
CA C:SER226 4.9 22.5 1.0
CA C:GLY222 4.9 30.1 1.0
CA C:VAL195 5.0 17.8 1.0
CG C:TYR225 5.0 22.5 1.0

Potassium binding site 7 out of 8 in 5tht

Go back to Potassium Binding Sites List in 5tht
Potassium binding site 7 out of 8 in the Crystal Structure of G303A 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 7 of Crystal Structure of G303A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K403

b:20.5
occ:1.00
O D:ASP178 2.7 25.0 1.0
OD1 D:ASP176 2.8 16.1 1.0
O D:ASP176 2.8 16.1 1.0
O D:HIS180 2.8 22.7 1.0
O D:LEU200 2.9 23.2 1.0
OG D:SER199 3.0 20.6 1.0
CG D:ASP176 3.4 20.7 1.0
C D:ASP176 3.4 19.0 1.0
N D:ASP178 3.5 23.0 1.0
C D:ASP178 3.6 23.2 1.0
C D:LEU200 3.7 22.3 1.0
CB D:ASP176 3.7 17.8 1.0
CB D:HIS201 3.7 22.8 1.0
C D:HIS180 3.8 23.7 1.0
CA D:ASP178 3.9 19.8 1.0
N D:LEU200 4.0 16.6 1.0
C D:LEU177 4.0 22.1 1.0
CB D:ASP178 4.1 18.8 1.0
N D:LEU177 4.1 17.2 1.0
CB D:SER199 4.1 18.6 1.0
CA D:ASP176 4.2 14.1 1.0
OD2 D:ASP176 4.2 21.3 1.0
CA D:LEU177 4.2 17.2 1.0
CA D:HIS201 4.2 20.4 1.0
N D:GLY182 4.3 23.8 1.0
N D:HIS201 4.3 24.1 1.0
ND1 D:HIS201 4.4 22.0 1.0
CA D:SER199 4.4 17.5 1.0
CA D:HIS181 4.4 25.6 1.0
C D:SER199 4.5 20.7 1.0
N D:HIS181 4.5 23.3 1.0
CG D:HIS201 4.5 23.9 1.0
CA D:LEU200 4.5 20.5 1.0
N D:HIS180 4.5 20.7 1.0
O D:HOH505 4.6 17.7 1.0
C D:HIS181 4.7 21.8 1.0
C D:LEU179 4.7 26.7 1.0
N D:LEU179 4.7 19.5 1.0
CE1 D:HIS142 4.7 23.6 1.0
O D:LEU177 4.8 22.1 1.0
CA D:HIS180 4.8 25.4 1.0
O D:LEU179 5.0 21.8 1.0

Potassium binding site 8 out of 8 in 5tht

Go back to Potassium Binding Sites List in 5tht
Potassium binding site 8 out of 8 in the Crystal Structure of G303A 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 8 of Crystal Structure of G303A HDAC8 in Complex with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K404

b:26.5
occ:1.00
O D:PHE189 2.6 24.9 1.0
O D:VAL195 2.6 23.0 1.0
O D:HOH502 2.8 24.7 1.0
O D:TYR225 2.9 30.1 1.0
O D:THR192 3.0 30.3 1.0
O D:HOH525 3.1 23.9 1.0
CB D:TYR225 3.5 30.6 1.0
C D:PHE189 3.6 25.9 1.0
C D:TYR225 3.6 29.6 1.0
C D:VAL195 3.9 24.9 1.0
OG D:SER226 3.9 27.7 1.0
CB D:PHE189 4.2 21.6 1.0
C D:THR192 4.2 27.6 1.0
CA D:TYR225 4.2 27.3 1.0
CA D:SER190 4.2 28.0 1.0
CA D:MET196 4.3 25.6 1.0
N D:SER190 4.3 22.2 1.0
O D:GLY222 4.4 31.5 1.0
N D:SER226 4.5 26.5 1.0
CA D:PHE189 4.5 27.3 1.0
C D:SER190 4.5 30.3 1.0
N D:MET196 4.5 24.3 1.0
CG2 D:THR192 4.6 21.0 1.0
O D:SER190 4.7 26.0 1.0
N D:THR197 4.7 25.2 1.0
N D:THR192 4.7 25.4 1.0
CG D:TYR225 4.8 28.5 1.0
CA D:GLY222 4.9 32.2 1.0
CA D:SER226 5.0 27.4 1.0
CA D:VAL195 5.0 21.3 1.0
C D:MET196 5.0 24.2 1.0
CG2 D:THR197 5.0 20.5 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 00:07:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy