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

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