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Potassium in PDB 5d1d: Crystal Structure of P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

Enzymatic activity of Crystal Structure of P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5d1d was solved by C.Decroos, N.H.Christianson, L.E.Gullett, C.M.Bowman, 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) 44.50 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.281, 97.987, 105.933, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.6

Other elements in 5d1d:

The structure of Crystal Structure of P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5d1d). 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 P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5d1d:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5d1d

Go back to Potassium Binding Sites List in 5d1d
Potassium binding site 1 out of 4 in the Crystal Structure of P91L-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 P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:24.8
occ:1.00
 O A:LEU200 2.7 21.8 1.0
O A:ASP178 2.7 22.0 1.0
O A:ASP176 2.8 23.2 1.0
OD1 A:ASP176 2.8 26.3 1.0
O A:HIS180 2.8 19.9 1.0
OG A:SER199 2.9 25.1 1.0
C A:ASP176 3.4 25.2 1.0
N A:ASP178 3.4 24.3 1.0
CG A:ASP176 3.4 27.0 1.0
C A:ASP178 3.5 23.1 1.0
C A:LEU200 3.6 22.6 1.0
CB A:ASP176 3.8 22.9 1.0
CB A:HIS201 3.8 23.0 1.0
C A:HIS180 3.8 21.7 1.0
CA A:ASP178 3.8 23.3 1.0
N A:LEU200 3.9 23.0 1.0
CB A:ASP178 3.9 23.4 1.0
C A:LEU177 4.0 26.0 1.0
N A:LEU177 4.0 23.7 1.0
CB A:SER199 4.1 24.9 1.0
CA A:LEU177 4.2 23.4 1.0
CA A:ASP176 4.2 26.7 1.0
ND1 A:HIS201 4.3 24.5 1.0
CA A:HIS201 4.3 25.8 1.0
N A:HIS201 4.3 22.0 1.0
CA A:SER199 4.4 27.2 1.0
N A:GLY182 4.4 22.3 1.0
OD2 A:ASP176 4.4 34.2 1.0
C A:SER199 4.4 25.6 1.0
CA A:LEU200 4.4 25.8 1.0
CA A:HIS181 4.5 21.2 1.0
N A:HIS180 4.5 23.3 1.0
O A:HOH544 4.5 23.7 1.0
CG A:HIS201 4.5 23.2 1.0
N A:HIS181 4.5 20.2 1.0
N A:LEU179 4.7 22.4 1.0
C A:LEU179 4.7 24.1 1.0
CE1 A:HIS142 4.7 24.0 1.0
O A:LEU177 4.8 22.1 1.0
CA A:HIS180 4.8 23.5 1.0
C A:HIS181 4.8 23.2 1.0

Potassium binding site 2 out of 4 in 5d1d

Go back to Potassium Binding Sites List in 5d1d
Potassium binding site 2 out of 4 in the Crystal Structure of P91L-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 P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:26.8
occ:1.00
 O A:PHE189 2.6 27.8 1.0
O A:VAL195 2.6 27.5 1.0
O A:HOH524 2.7 23.8 1.0
O A:THR192 2.8 27.4 1.0
O A:HOH576 3.0 27.1 1.0
O A:TYR225 3.0 30.0 1.0
C A:PHE189 3.6 24.0 1.0
CB A:TYR225 3.7 28.8 1.0
C A:TYR225 3.7 29.7 1.0
C A:VAL195 3.8 26.1 1.0
OG A:SER226 3.9 28.9 1.0
C A:THR192 4.0 29.2 1.0
CB A:PHE189 4.1 27.3 1.0
CA A:SER190 4.3 28.1 0.5
CA A:SER190 4.3 28.9 0.5
CA A:TYR225 4.3 27.8 1.0
N A:SER190 4.3 26.2 0.5
N A:SER190 4.3 27.2 0.5
CG2 A:THR192 4.4 26.0 1.0
CA A:MET196 4.4 29.5 1.0
O A:SER190 4.4 28.6 0.5
O A:GLY222 4.4 26.3 1.0
C A:SER190 4.5 28.9 0.5
N A:SER226 4.5 26.9 1.0
CA A:PHE189 4.5 26.4 1.0
C A:SER190 4.5 29.2 0.5
N A:THR192 4.5 29.0 1.0
N A:MET196 4.6 28.1 1.0
O A:SER190 4.6 28.9 0.5
N A:THR197 4.6 27.6 1.0
CA A:THR192 4.8 23.7 1.0
CA A:VAL195 4.9 26.7 1.0
CA A:GLY222 4.9 28.5 1.0
CA A:SER226 4.9 30.2 1.0
CG A:TYR225 5.0 29.0 1.0
CG2 A:THR197 5.0 28.4 1.0

Potassium binding site 3 out of 4 in 5d1d

Go back to Potassium Binding Sites List in 5d1d
Potassium binding site 3 out of 4 in the Crystal Structure of P91L-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 P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:23.5
occ:1.00
 O B:ASP178 2.6 21.0 1.0
O B:LEU200 2.7 23.2 1.0
OD1 B:ASP176 2.7 25.5 1.0
O B:ASP176 2.8 24.5 1.0
O B:HIS180 2.8 19.7 1.0
OG B:SER199 3.0 27.0 1.0
N B:ASP178 3.4 23.7 1.0
CG B:ASP176 3.4 26.3 1.0
C B:ASP176 3.4 23.7 1.0
C B:ASP178 3.5 27.0 1.0
C B:LEU200 3.6 24.7 1.0
CB B:HIS201 3.7 20.4 1.0
CA B:ASP178 3.8 23.1 1.0
CB B:ASP176 3.8 23.5 1.0
C B:HIS180 3.8 23.4 1.0
CB B:ASP178 3.9 22.5 1.0
C B:LEU177 3.9 24.8 1.0
N B:LEU200 4.0 23.3 1.0
N B:LEU177 4.0 21.7 1.0
CA B:LEU177 4.2 23.3 1.0
CB B:SER199 4.2 26.3 1.0
CA B:ASP176 4.3 24.0 1.0
CA B:HIS201 4.3 24.5 1.0
N B:HIS201 4.3 22.4 1.0
OD2 B:ASP176 4.3 31.4 1.0
ND1 B:HIS201 4.3 22.2 1.0
CA B:SER199 4.4 27.9 1.0
CA B:LEU200 4.4 24.7 1.0
N B:GLY182 4.4 23.5 1.0
C B:SER199 4.5 25.2 1.0
CA B:HIS181 4.5 20.8 1.0
N B:HIS180 4.5 20.1 1.0
O B:HOH521 4.5 22.7 1.0
CG B:HIS201 4.5 21.7 1.0
N B:HIS181 4.6 18.1 1.0
N B:LEU179 4.6 22.8 1.0
C B:LEU179 4.7 25.0 1.0
O B:LEU177 4.7 24.3 1.0
CE1 B:HIS142 4.8 24.1 1.0
CA B:HIS180 4.8 21.1 1.0
C B:HIS181 4.9 23.5 1.0
O B:LEU179 5.0 21.2 1.0

Potassium binding site 4 out of 4 in 5d1d

Go back to Potassium Binding Sites List in 5d1d
Potassium binding site 4 out of 4 in the Crystal Structure of P91L-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 P91L-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:26.7
occ:1.00
 O B:VAL195 2.6 26.7 1.0
O B:PHE189 2.7 26.2 1.0
O B:HOH502 2.8 26.2 1.0
O B:HOH519 2.9 27.1 1.0
O B:THR192 2.9 31.7 1.0
O B:TYR225 3.0 28.0 1.0
CB B:TYR225 3.7 29.6 1.0
C B:TYR225 3.7 29.6 1.0
C B:PHE189 3.7 28.3 1.0
C B:VAL195 3.8 24.6 1.0
OG B:SER226 3.9 30.7 1.0
C B:THR192 4.1 33.8 1.0
CB B:PHE189 4.1 24.3 1.0
CA B:TYR225 4.3 29.4 1.0
CG2 B:THR192 4.3 27.9 1.0
CA B:MET196 4.4 25.7 1.0
N B:SER226 4.4 28.6 1.0
N B:SER190 4.5 24.0 1.0
O B:GLY222 4.5 29.5 1.0
CA B:PHE189 4.5 26.1 1.0
CA B:SER190 4.5 26.8 1.0
N B:MET196 4.6 26.2 1.0
O B:SER190 4.6 31.3 1.0
N B:THR192 4.6 32.3 1.0
C B:SER190 4.6 30.9 1.0
N B:THR197 4.6 25.5 1.0
OG1 B:THR197 4.8 32.8 1.0
CA B:THR192 4.8 32.5 1.0
CA B:VAL195 4.8 26.0 1.0
CA B:SER226 4.9 27.9 1.0
CG B:TYR225 4.9 29.8 1.0
C B:MET196 5.0 28.4 1.0
CB B:SER226 5.0 27.8 1.0

Reference:

C.Decroos, N.H.Christianson, L.E.Gullett, C.M.Bowman, K.E.Christianson, M.A.Deardorff, D.W.Christianson. Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia De Lange Syndrome Spectrum Disorders. Biochemistry V. 54 6501 2015.
ISSN: ISSN 0006-2960
PubMed: 26463496
DOI: 10.1021/ACS.BIOCHEM.5B00881
Page generated: Mon Aug 12 13:09:37 2024

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