Atomistry » Potassium » PDB 7fs1-7k5g » 7jvu
Atomistry »
  Potassium »
    PDB 7fs1-7k5g »
      7jvu »

Potassium in PDB 7jvu: Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha

Enzymatic activity of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha

All present enzymatic activity of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha, PDB code: 7jvu was solved by J.D.Osko, D.W.Christianson, C.Decroos, N.J.Porter, M.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.314, 84.118, 94.281, 90.00, 99.06, 90.00
R / Rfree (%) 16.4 / 18.5

Other elements in 7jvu:

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha (pdb code 7jvu). 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 Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha, PDB code: 7jvu:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 7jvu

Go back to Potassium Binding Sites List in 7jvu
Potassium binding site 1 out of 4 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha


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 Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:12.4
occ:1.00
 O A:LEU200 2.6 14.0 1.0
O A:ASP178 2.7 13.0 1.0
OD1 A:ASP176 2.7 13.4 1.0
O A:HIS180 2.7 12.0 1.0
O A:ASP176 2.8 11.9 1.0
OG A:SER199 2.9 14.1 1.0
CG A:ASP176 3.4 13.6 1.0
C A:ASP176 3.4 11.8 1.0
N A:ASP178 3.5 12.7 1.0
C A:ASP178 3.5 11.6 1.0
C A:LEU200 3.6 11.1 1.0
C A:HIS180 3.7 10.5 1.0
CB A:HIS201 3.8 12.3 1.0
CB A:ASP176 3.9 12.5 1.0
CA A:ASP178 3.9 12.6 1.0
N A:LEU200 3.9 13.1 1.0
CB A:ASP178 3.9 12.9 1.0
C A:LEU177 4.0 13.1 1.0
N A:LEU177 4.0 12.2 1.0
CB A:SER199 4.1 14.9 1.0
CA A:LEU177 4.2 11.1 1.0
CA A:ASP176 4.3 12.6 1.0
ND1 A:HIS201 4.3 13.7 1.0
CA A:HIS201 4.3 11.3 1.0
OD2 A:ASP176 4.3 14.3 1.0
N A:GLY182 4.4 12.8 1.0
CA A:SER199 4.4 12.5 1.0
N A:HIS201 4.4 12.0 1.0
N A:HIS180 4.4 11.4 1.0
CA A:HIS181 4.4 11.9 1.0
N A:HIS181 4.4 11.9 1.0
CA A:LEU200 4.5 12.1 1.0
C A:SER199 4.5 13.3 1.0
CG A:HIS201 4.5 12.1 1.0
O A:HOH550 4.6 14.2 1.0
C A:LEU179 4.7 11.7 1.0
CA A:HIS180 4.7 12.6 1.0
C A:HIS181 4.7 13.3 1.0
N A:LEU179 4.7 11.7 1.0
O A:LEU177 4.7 13.8 1.0
CE1 A:HIS142 4.9 13.5 1.0

Potassium binding site 2 out of 4 in 7jvu

Go back to Potassium Binding Sites List in 7jvu
Potassium binding site 2 out of 4 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha


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 Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:17.1
occ:1.00
 O A:VAL195 2.6 17.2 1.0
O A:PHE189 2.6 16.8 1.0
O A:THR192 2.8 21.1 1.0
O A:HOH580 2.8 17.0 1.0
O A:HOH698 2.8 18.1 1.0
O A:TYR225 3.1 18.5 1.0
C A:PHE189 3.6 17.5 1.0
CB A:TYR225 3.6 17.5 1.0
C A:TYR225 3.7 17.4 1.0
C A:VAL195 3.8 15.1 1.0
C A:THR192 4.0 19.1 1.0
CB A:PHE189 4.0 16.3 1.0
OG A:SER226 4.1 18.5 1.0
CA A:TYR225 4.3 17.2 1.0
CA A:PHE189 4.4 16.5 1.0
CG2 A:THR192 4.4 23.2 1.0
N A:SER190 4.4 16.6 1.0
CA A:MET196 4.4 17.5 1.0
O A:SER190 4.5 18.7 1.0
CA A:SER190 4.5 17.1 1.0
N A:SER226 4.5 17.0 1.0
C A:SER190 4.5 19.1 1.0
N A:THR192 4.5 19.1 1.0
O A:GLY222 4.6 19.3 1.0
N A:MET196 4.6 14.8 1.0
N A:THR197 4.7 14.9 1.0
CA A:THR192 4.8 19.4 1.0
CA A:VAL195 4.8 18.6 1.0
CG A:TYR225 4.9 18.7 1.0
CA A:GLY222 4.9 18.2 1.0
N A:SER193 4.9 20.9 1.0
N A:VAL195 5.0 16.9 1.0
CB A:VAL195 5.0 18.2 1.0

Potassium binding site 3 out of 4 in 7jvu

Go back to Potassium Binding Sites List in 7jvu
Potassium binding site 3 out of 4 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha


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 Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:12.1
occ:1.00
 O B:LEU200 2.6 13.1 1.0
OD1 B:ASP176 2.7 12.8 1.0
O B:ASP178 2.7 13.6 1.0
O B:HIS180 2.8 12.3 1.0
O B:ASP176 2.8 13.6 1.0
OG B:SER199 2.9 14.1 1.0
CG B:ASP176 3.4 12.7 1.0
C B:ASP176 3.4 12.6 1.0
N B:ASP178 3.5 12.1 1.0
C B:ASP178 3.6 12.4 1.0
C B:LEU200 3.6 12.2 1.0
C B:HIS180 3.7 12.1 1.0
CB B:HIS201 3.8 11.6 1.0
CA B:ASP178 3.9 12.4 1.0
CB B:ASP176 3.9 12.6 1.0
N B:LEU200 3.9 12.4 1.0
CB B:ASP178 4.0 13.6 1.0
C B:LEU177 4.0 10.6 1.0
N B:LEU177 4.1 11.4 1.0
CB B:SER199 4.1 14.3 1.0
CA B:LEU177 4.2 12.1 1.0
CA B:ASP176 4.3 13.0 1.0
CA B:HIS201 4.3 12.1 1.0
ND1 B:HIS201 4.3 14.1 1.0
OD2 B:ASP176 4.3 15.1 1.0
N B:GLY182 4.4 13.0 1.0
CA B:SER199 4.4 13.3 1.0
N B:HIS201 4.4 12.7 1.0
CA B:HIS181 4.4 13.2 1.0
N B:HIS180 4.4 12.4 1.0
N B:HIS181 4.5 11.5 1.0
CA B:LEU200 4.5 13.0 1.0
C B:SER199 4.5 14.8 1.0
CG B:HIS201 4.5 13.0 1.0
O B:HOH585 4.5 13.1 1.0
C B:LEU179 4.7 13.0 1.0
C B:HIS181 4.7 12.2 1.0
CA B:HIS180 4.7 12.6 1.0
N B:LEU179 4.7 11.6 1.0
O B:LEU177 4.7 13.4 1.0
CE1 B:HIS142 4.9 13.5 1.0
O B:LEU179 5.0 11.9 1.0

Potassium binding site 4 out of 4 in 7jvu

Go back to Potassium Binding Sites List in 7jvu
Potassium binding site 4 out of 4 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha


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 Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:17.3
occ:1.00
 O B:PHE189 2.6 16.3 1.0
O B:VAL195 2.6 18.4 1.0
O B:HOH579 2.7 17.5 1.0
O B:THR192 2.8 18.2 1.0
O B:HOH681 2.9 18.2 1.0
O B:TYR225 3.1 17.9 1.0
C B:PHE189 3.6 15.7 1.0
CB B:TYR225 3.6 19.2 1.0
C B:TYR225 3.7 17.4 1.0
C B:VAL195 3.8 16.2 1.0
CB B:PHE189 4.0 15.8 1.0
C B:THR192 4.0 18.8 1.0
OG B:SER226 4.1 17.2 1.0
CA B:TYR225 4.3 15.9 1.0
CA B:SER190 4.3 15.9 0.4
O B:SER190 4.4 16.4 0.6
CG2 B:THR192 4.4 16.6 1.0
N B:SER190 4.4 16.4 0.4
N B:SER190 4.4 16.4 0.6
CA B:SER190 4.4 15.8 0.6
CA B:PHE189 4.4 15.8 1.0
C B:SER190 4.4 16.0 0.6
CA B:MET196 4.4 16.4 1.0
N B:SER226 4.5 15.5 1.0
N B:THR192 4.5 18.1 1.0
C B:SER190 4.6 16.1 0.4
N B:MET196 4.6 14.5 1.0
O B:GLY222 4.6 18.0 1.0
N B:THR197 4.7 14.2 1.0
CA B:THR192 4.8 16.9 1.0
CA B:VAL195 4.8 17.5 1.0
O B:SER190 4.8 17.2 0.4
CG B:TYR225 4.9 19.0 1.0
CA B:GLY222 4.9 21.2 1.0
N B:VAL195 4.9 16.8 1.0
CB B:VAL195 4.9 17.2 1.0
OG1 B:THR197 5.0 15.9 1.0

Reference:

J.D.Osko, N.J.Porter, C.Decroos, M.Lee, P.Watson, M.Deardorff, D.W.Christianson. Structural Analysis of Histone Deacetylase 8 Mutants Associated with Cornelia De Lange Syndrome Spectrum Disorders J.Struct.Biol. 2020.
ISSN: ESSN 1095-8657
Page generated: Mon Aug 12 19:08:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy