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Potassium in PDB 7jvw: Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344

Enzymatic activity of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344

All present enzymatic activity of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344, PDB code: 7jvw 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) 48.99 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.980, 82.750, 94.520, 90.00, 98.84, 90.00
R / Rfree (%) 19.5 / 25.4

Other elements in 7jvw:

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed 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 Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344 (pdb code 7jvw). 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) G320R Mutation Complexed with M344, PDB code: 7jvw:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 7jvw

Go back to Potassium Binding Sites List in 7jvw
Potassium binding site 1 out of 4 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed 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 Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:29.1
occ:1.00
 OD1 A:ASP176 2.6 26.9 1.0
O A:LEU200 2.6 26.0 1.0
O A:ASP176 2.8 26.1 1.0
O A:HIS180 2.8 24.2 1.0
O A:ASP178 2.9 26.6 1.0
OG A:SER199 3.1 28.6 1.0
N A:ASP178 3.3 29.7 1.0
C A:ASP176 3.3 30.0 1.0
CG A:ASP176 3.4 32.7 1.0
C A:LEU200 3.5 29.3 1.0
C A:ASP178 3.6 32.1 1.0
N A:LEU177 3.7 28.9 1.0
C A:LEU177 3.8 31.8 1.0
CB A:ASP176 3.8 25.8 1.0
CA A:ASP178 3.8 26.2 1.0
N A:LEU200 3.8 30.3 1.0
CB A:HIS201 3.9 28.5 1.0
CB A:ASP178 3.9 19.6 1.0
C A:HIS180 3.9 28.3 1.0
CA A:LEU177 3.9 32.1 1.0
CA A:ASP176 4.1 28.0 1.0
CB A:SER199 4.2 27.0 1.0
CA A:SER199 4.3 33.2 1.0
CA A:HIS201 4.3 29.8 1.0
CA A:LEU200 4.3 31.3 1.0
N A:HIS201 4.4 29.7 1.0
OD2 A:ASP176 4.4 33.3 1.0
C A:SER199 4.4 34.1 1.0
N A:GLY182 4.5 24.9 1.0
ND1 A:HIS201 4.5 34.4 1.0
O A:HOH632 4.5 18.1 1.0
O A:LEU177 4.6 28.8 1.0
N A:HIS180 4.6 28.5 1.0
CA A:HIS181 4.6 29.8 1.0
CG A:HIS201 4.7 34.9 1.0
N A:HIS181 4.7 20.4 1.0
N A:LEU179 4.8 32.4 1.0
C A:LEU179 4.8 28.8 1.0
C A:HIS181 4.9 26.7 1.0
CE1 A:HIS142 4.9 24.6 1.0
CA A:HIS180 4.9 27.7 1.0

Potassium binding site 2 out of 4 in 7jvw

Go back to Potassium Binding Sites List in 7jvw
Potassium binding site 2 out of 4 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed 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 Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:38.6
occ:1.00
 O A:VAL195 2.5 27.0 1.0
O A:PHE189 2.6 35.4 1.0
O A:HOH620 2.8 35.9 1.0
O A:HOH638 3.0 29.8 1.0
O A:THR192 3.0 41.9 1.0
O A:TYR225 3.2 36.3 1.0
C A:PHE189 3.5 34.1 1.0
CB A:TYR225 3.6 41.1 1.0
C A:VAL195 3.7 34.0 1.0
C A:TYR225 3.8 34.8 1.0
CB A:PHE189 4.0 37.8 1.0
C A:THR192 4.1 35.0 1.0
CA A:SER190 4.2 38.5 1.0
CA A:MET196 4.3 27.9 1.0
CG2 A:THR192 4.3 38.0 1.0
N A:SER190 4.3 35.5 1.0
CA A:TYR225 4.4 40.5 1.0
OG A:SER226 4.4 31.0 1.0
CA A:PHE189 4.4 32.4 1.0
N A:MET196 4.5 31.0 1.0
N A:SER226 4.5 35.7 1.0
N A:THR192 4.5 35.1 1.0
C A:SER190 4.5 40.8 1.0
N A:THR197 4.5 34.9 1.0
O A:GLY222 4.6 40.3 1.0
CA A:VAL195 4.8 35.6 1.0
OG1 A:THR197 4.8 35.9 1.0
O A:SER190 4.8 39.3 1.0
CA A:THR192 4.8 37.6 1.0
CG A:TYR225 4.9 40.8 1.0
C A:MET196 4.9 32.6 1.0
CA A:GLY222 5.0 41.6 1.0
N A:VAL195 5.0 34.2 1.0
CB A:VAL195 5.0 35.1 1.0

Potassium binding site 3 out of 4 in 7jvw

Go back to Potassium Binding Sites List in 7jvw
Potassium binding site 3 out of 4 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed 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 Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:30.4
occ:1.00
 O B:LEU200 2.6 31.4 1.0
O B:ASP176 2.6 28.1 1.0
O B:HIS180 2.7 31.6 1.0
O B:ASP178 2.8 25.4 1.0
OG B:SER199 2.9 23.6 1.0
OD1 B:ASP176 3.0 40.8 1.0
C B:ASP176 3.3 29.9 1.0
N B:ASP178 3.5 32.8 1.0
C B:LEU200 3.5 28.8 1.0
CG B:ASP176 3.6 39.2 1.0
C B:ASP178 3.6 31.3 1.0
C B:HIS180 3.7 30.9 1.0
CB B:ASP176 3.7 33.5 1.0
CB B:HIS201 3.8 27.9 1.0
N B:LEU200 3.8 32.5 1.0
CA B:ASP178 3.9 25.4 1.0
CB B:ASP178 3.9 28.9 1.0
C B:LEU177 4.0 32.5 1.0
N B:LEU177 4.0 34.0 1.0
CB B:SER199 4.1 29.4 1.0
CA B:ASP176 4.2 26.7 1.0
CA B:LEU177 4.2 36.4 1.0
CA B:HIS201 4.2 25.0 1.0
ND1 B:HIS201 4.3 28.8 1.0
N B:GLY182 4.3 27.9 1.0
N B:HIS201 4.3 27.9 1.0
CA B:HIS181 4.3 28.7 1.0
CA B:LEU200 4.3 31.4 1.0
CA B:SER199 4.4 32.9 1.0
C B:SER199 4.4 33.0 1.0
N B:HIS181 4.4 28.2 1.0
N B:HIS180 4.4 33.9 1.0
CG B:HIS201 4.5 33.6 1.0
OD2 B:ASP176 4.6 35.8 1.0
CA B:HIS180 4.7 28.8 1.0
C B:HIS181 4.7 28.5 1.0
C B:LEU179 4.7 33.6 1.0
O B:HOH506 4.7 28.6 1.0
N B:LEU179 4.8 33.0 1.0
CE1 B:HIS142 4.8 26.9 1.0
O B:LEU177 4.8 30.0 1.0

Potassium binding site 4 out of 4 in 7jvw

Go back to Potassium Binding Sites List in 7jvw
Potassium binding site 4 out of 4 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed 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 Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:38.9
occ:1.00
 O B:PHE189 2.6 37.6 1.0
O B:VAL195 2.6 40.1 1.0
O B:THR192 2.7 48.4 1.0
O B:HOH536 2.8 35.0 1.0
O B:HOH539 3.0 30.2 1.0
O B:TYR225 3.1 42.3 1.0
CB B:TYR225 3.6 44.7 1.0
C B:PHE189 3.6 31.4 1.0
C B:TYR225 3.7 40.4 1.0
C B:VAL195 3.8 40.0 1.0
C B:THR192 3.9 47.6 1.0
CB B:PHE189 4.1 32.0 1.0
CA B:TYR225 4.3 41.4 1.0
CA B:SER190 4.3 40.6 1.0
CA B:MET196 4.4 45.8 1.0
N B:THR192 4.4 33.3 1.0
N B:SER226 4.4 39.6 1.0
N B:SER190 4.4 29.1 1.0
C B:SER190 4.5 40.6 1.0
CA B:PHE189 4.5 36.5 1.0
OG B:SER226 4.5 30.8 1.0
N B:MET196 4.6 39.9 1.0
N B:THR197 4.6 32.4 1.0
O B:SER190 4.6 41.8 1.0
O B:GLY222 4.6 49.5 1.0
CA B:THR192 4.6 40.7 1.0
CG B:TYR225 4.8 42.6 1.0
CA B:VAL195 4.9 41.8 1.0
CA B:GLY222 4.9 39.3 1.0
N B:SER193 4.9 47.6 1.0
CB B:THR192 4.9 45.0 1.0
C B:MET196 5.0 36.4 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 19:09:38 2024

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