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Potassium in PDB 4qa5: Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

Enzymatic activity of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa5 was solved by C.Decroos, C.B.Bowman, J.-A.S.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.42 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.830, 97.760, 105.485, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.4

Other elements in 4qa5:

The structure of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 4qa5). 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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa5:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4qa5

Go back to Potassium Binding Sites List in 4qa5
Potassium binding site 1 out of 4 in the Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:16.0
occ:1.00
 OD1 A:ASP176 2.7 16.9 1.0
O A:ASP178 2.7 14.5 1.0
O A:LEU200 2.7 16.7 1.0
O A:HIS180 2.8 14.7 1.0
O A:ASP176 2.9 16.2 1.0
OG A:SER199 2.9 18.7 1.0
N A:ASP178 3.4 15.3 1.0
CG A:ASP176 3.4 19.4 1.0
C A:ASP176 3.5 17.4 1.0
C A:ASP178 3.6 16.2 1.0
C A:LEU200 3.6 14.8 1.0
C A:HIS180 3.8 13.7 1.0
CB A:HIS201 3.8 17.8 1.0
CA A:ASP178 3.9 14.0 1.0
CB A:ASP176 3.9 15.1 1.0
CB A:ASP178 3.9 15.9 1.0
N A:LEU200 3.9 15.2 1.0
C A:LEU177 4.0 12.9 1.0
N A:LEU177 4.0 14.9 1.0
CB A:SER199 4.1 17.7 1.0
CA A:LEU177 4.2 13.8 1.0
ND1 A:HIS201 4.3 16.9 1.0
CA A:ASP176 4.3 15.0 1.0
N A:GLY182 4.3 16.1 1.0
OD2 A:ASP176 4.4 19.5 1.0
CA A:HIS201 4.4 15.5 1.0
CA A:SER199 4.4 16.1 1.0
N A:HIS201 4.4 16.9 1.0
C A:SER199 4.5 18.0 1.0
CA A:LEU200 4.5 16.9 1.0
N A:HIS180 4.5 14.1 1.0
O A:HOH504 4.5 16.2 1.0
CA A:HIS181 4.5 16.3 1.0
CG A:HIS201 4.5 15.0 1.0
N A:HIS181 4.6 15.1 1.0
C A:LEU179 4.7 16.1 1.0
N A:LEU179 4.7 13.0 1.0
C A:HIS181 4.7 14.3 1.0
O A:LEU177 4.8 15.3 1.0
CA A:HIS180 4.8 11.9 1.0
CE1 A:HIS142 4.8 15.5 1.0

Potassium binding site 2 out of 4 in 4qa5

Go back to Potassium Binding Sites List in 4qa5
Potassium binding site 2 out of 4 in the Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:22.5
occ:1.00
 O A:PHE189 2.6 23.1 1.0
O A:VAL195 2.6 24.3 1.0
O A:HOH522 2.7 22.6 1.0
O A:THR192 2.8 24.5 1.0
O A:HOH516 2.8 21.6 1.0
O A:TYR225 3.1 22.4 1.0
C A:PHE189 3.6 20.5 1.0
CB A:TYR225 3.6 23.0 1.0
C A:TYR225 3.7 20.5 1.0
C A:VAL195 3.8 20.9 1.0
C A:THR192 4.0 28.1 1.0
OG A:SER226 4.0 25.4 1.0
CB A:PHE189 4.1 21.9 1.0
CA A:TYR225 4.3 21.7 1.0
CA A:MET196 4.4 21.7 0.5
CA A:SER190 4.4 19.0 1.0
N A:SER190 4.4 22.0 1.0
CA A:MET196 4.4 21.7 0.5
O A:SER190 4.4 27.0 1.0
C A:SER190 4.5 28.2 1.0
N A:SER226 4.5 19.5 1.0
CA A:PHE189 4.5 23.8 1.0
N A:THR192 4.5 24.8 1.0
CG2 A:THR192 4.5 21.6 1.0
O A:GLY222 4.6 23.1 1.0
N A:MET196 4.6 22.3 1.0
N A:THR197 4.7 20.7 1.0
CA A:THR192 4.8 25.2 1.0
CA A:VAL195 4.8 22.1 1.0
CA A:GLY222 4.8 23.3 1.0
OG1 A:THR197 4.9 20.7 1.0
CG A:TYR225 4.9 23.1 1.0
CA A:SER226 5.0 21.6 1.0
N A:VAL195 5.0 22.3 1.0
C A:MET196 5.0 20.3 1.0
CB A:VAL195 5.0 22.9 1.0

Potassium binding site 3 out of 4 in 4qa5

Go back to Potassium Binding Sites List in 4qa5
Potassium binding site 3 out of 4 in the Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:16.3
occ:1.00
 O B:ASP178 2.6 14.2 1.0
O B:LEU200 2.7 15.0 1.0
OD1 B:ASP176 2.7 15.7 1.0
O B:HIS180 2.8 16.1 1.0
O B:ASP176 2.8 16.1 1.0
OG B:SER199 2.9 18.0 1.0
C B:ASP176 3.4 13.5 1.0
CG B:ASP176 3.4 18.9 1.0
N B:ASP178 3.4 14.6 1.0
C B:ASP178 3.5 12.1 1.0
C B:LEU200 3.6 15.7 1.0
C B:HIS180 3.8 14.3 1.0
CB B:HIS201 3.8 14.8 1.0
CA B:ASP178 3.8 14.5 1.0
CB B:ASP176 3.9 12.6 1.0
CB B:ASP178 3.9 15.9 1.0
N B:LEU200 3.9 14.8 1.0
C B:LEU177 3.9 14.9 1.0
N B:LEU177 4.0 14.2 1.0
CB B:SER199 4.1 17.0 1.0
CA B:LEU177 4.1 14.9 1.0
CA B:ASP176 4.3 15.9 1.0
OD2 B:ASP176 4.3 17.8 1.0
ND1 B:HIS201 4.3 17.6 1.0
CA B:HIS201 4.4 16.7 1.0
N B:GLY182 4.4 16.9 1.0
N B:HIS201 4.4 18.5 1.0
N B:HIS180 4.4 14.8 1.0
CA B:SER199 4.4 15.9 1.0
CA B:HIS181 4.5 16.9 1.0
CA B:LEU200 4.5 15.0 1.0
C B:SER199 4.5 14.3 1.0
N B:HIS181 4.5 13.1 1.0
O B:HOH502 4.5 18.0 1.0
CG B:HIS201 4.6 17.3 1.0
C B:LEU179 4.7 16.4 1.0
N B:LEU179 4.7 13.1 1.0
C B:HIS181 4.7 17.2 1.0
CA B:HIS180 4.7 13.1 1.0
O B:LEU177 4.8 16.5 1.0
CE1 B:HIS142 4.8 17.9 1.0
O B:LEU179 5.0 17.3 1.0

Potassium binding site 4 out of 4 in 4qa5

Go back to Potassium Binding Sites List in 4qa5
Potassium binding site 4 out of 4 in the Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:20.8
occ:1.00
 O B:VAL195 2.6 19.6 1.0
O B:PHE189 2.6 20.8 1.0
O B:HOH510 2.8 18.3 1.0
O B:THR192 2.8 22.4 1.0
O B:HOH518 2.8 19.4 1.0
O B:TYR225 3.0 19.1 1.0
C B:PHE189 3.6 20.0 1.0
CB B:TYR225 3.6 19.6 1.0
C B:TYR225 3.7 22.7 1.0
C B:VAL195 3.8 17.6 1.0
OG B:SER226 4.0 23.1 1.0
C B:THR192 4.0 25.0 1.0
CB B:PHE189 4.0 20.0 1.0
CA B:TYR225 4.3 21.4 1.0
CA B:MET196 4.4 18.3 1.0
CA B:PHE189 4.4 19.2 1.0
O B:SER190 4.4 23.6 1.0
N B:SER190 4.4 17.0 1.0
CA B:SER190 4.5 18.7 1.0
N B:SER226 4.5 17.9 1.0
C B:SER190 4.5 23.4 1.0
N B:THR192 4.6 22.0 1.0
N B:MET196 4.6 18.6 1.0
N B:THR197 4.7 18.4 1.0
O B:GLY222 4.7 21.8 1.0
CA B:THR192 4.8 25.7 1.0
CA B:VAL195 4.9 17.3 1.0
CG2 B:THR192 4.9 26.3 1.0
CG B:TYR225 4.9 21.8 1.0
N B:SER193 4.9 22.6 1.0
CA B:SER226 5.0 18.8 1.0
CB B:VAL195 5.0 16.5 1.0
C B:MET196 5.0 17.1 1.0
CA B:SER193 5.0 21.5 1.0

Reference:

C.Decroos, C.M.Bowman, J.A.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson. Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia De Lange Syndrome Spectrum Disorders. Acs Chem.Biol. V. 9 2157 2014.
ISSN: ISSN 1554-8929
PubMed: 25075551
DOI: 10.1021/CB5003762
Page generated: Mon Aug 12 11:51:22 2024

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