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Potassium in PDB 4qa0: Crystal Structure of C153F HDAC8 in Complex with Saha

Enzymatic activity of Crystal Structure of C153F HDAC8 in Complex with Saha

All present enzymatic activity of Crystal Structure of C153F HDAC8 in Complex with Saha:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of C153F HDAC8 in Complex with Saha, PDB code: 4qa0 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) 44.83 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.523, 84.751, 95.003, 90.00, 99.29, 90.00
R / Rfree (%) 17.8 / 21

Other elements in 4qa0:

The structure of Crystal Structure of C153F HDAC8 in Complex 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 C153F HDAC8 in Complex with Saha (pdb code 4qa0). 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 C153F HDAC8 in Complex with Saha, PDB code: 4qa0:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4qa0

Go back to Potassium Binding Sites List in 4qa0
Potassium binding site 1 out of 4 in the Crystal Structure of C153F HDAC8 in Complex 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 C153F HDAC8 in Complex with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:19.8
occ:1.00
 O A:LEU200 2.7 24.4 1.0
OD1 A:ASP176 2.7 21.6 1.0
O A:ASP178 2.7 17.6 1.0
O A:HIS180 2.8 20.0 1.0
O A:ASP176 2.8 23.3 1.0
OG A:SER199 3.0 21.9 1.0
N A:ASP178 3.3 22.9 1.0
C A:ASP176 3.4 21.3 1.0
CG A:ASP176 3.4 22.5 1.0
C A:ASP178 3.5 21.2 1.0
C A:LEU200 3.6 21.1 1.0
CB A:HIS201 3.7 20.4 1.0
CA A:ASP178 3.8 19.6 1.0
CB A:ASP176 3.8 20.4 1.0
C A:HIS180 3.8 20.3 1.0
CB A:ASP178 3.9 19.7 1.0
C A:LEU177 3.9 21.8 1.0
N A:LEU177 4.0 22.5 1.0
N A:LEU200 4.0 21.0 1.0
CA A:LEU177 4.1 22.2 1.0
CA A:ASP176 4.2 20.4 1.0
CB A:SER199 4.2 22.1 1.0
CA A:HIS201 4.3 21.0 1.0
OD2 A:ASP176 4.3 25.2 1.0
N A:HIS201 4.4 20.4 1.0
ND1 A:HIS201 4.4 21.2 1.0
CA A:HIS181 4.4 21.3 1.0
O A:HOH507 4.5 21.9 1.0
N A:GLY182 4.5 21.5 1.0
N A:HIS181 4.5 20.5 1.0
CA A:SER199 4.5 22.9 1.0
CA A:LEU200 4.5 22.6 1.0
N A:HIS180 4.5 18.7 1.0
C A:SER199 4.5 21.1 1.0
CG A:HIS201 4.5 20.4 1.0
N A:LEU179 4.7 21.6 1.0
O A:LEU177 4.7 20.8 1.0
C A:LEU179 4.7 21.8 1.0
CA A:HIS180 4.8 17.5 1.0
CE1 A:HIS142 4.8 21.6 1.0
C A:HIS181 4.8 21.7 1.0

Potassium binding site 2 out of 4 in 4qa0

Go back to Potassium Binding Sites List in 4qa0
Potassium binding site 2 out of 4 in the Crystal Structure of C153F HDAC8 in Complex 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 C153F HDAC8 in Complex with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:24.5
occ:1.00
 O A:VAL195 2.6 24.6 1.0
O A:PHE189 2.6 24.8 1.0
O A:HOH503 2.8 24.7 1.0
O A:THR192 2.8 27.2 1.0
O A:HOH501 2.9 21.8 1.0
O A:TYR225 2.9 27.9 1.0
C A:PHE189 3.6 23.9 1.0
CB A:TYR225 3.6 28.3 1.0
C A:TYR225 3.7 27.8 1.0
C A:VAL195 3.8 24.7 1.0
OG A:SER226 3.9 26.2 1.0
CB A:PHE189 4.0 25.0 1.0
C A:THR192 4.0 28.4 1.0
CA A:TYR225 4.3 25.4 1.0
N A:SER190 4.4 24.6 1.0
CA A:PHE189 4.4 24.3 1.0
O A:GLY222 4.5 31.4 1.0
CA A:MET196 4.5 25.9 1.0
CA A:SER190 4.5 28.6 1.0
N A:SER226 4.6 25.3 1.0
N A:THR192 4.6 27.7 1.0
C A:SER190 4.6 28.8 1.0
CG2 A:THR192 4.6 28.7 1.0
N A:MET196 4.6 24.2 1.0
N A:THR197 4.7 22.8 1.0
O A:SER190 4.7 26.7 1.0
OG1 A:THR197 4.8 29.8 1.0
CA A:THR192 4.8 26.1 1.0
CA A:VAL195 4.8 22.5 1.0
CA A:GLY222 4.9 29.9 1.0
N A:SER193 4.9 24.7 1.0
CG A:TYR225 4.9 26.4 1.0
CA A:SER193 5.0 28.8 1.0
CB A:VAL195 5.0 23.1 1.0

Potassium binding site 3 out of 4 in 4qa0

Go back to Potassium Binding Sites List in 4qa0
Potassium binding site 3 out of 4 in the Crystal Structure of C153F HDAC8 in Complex 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 C153F HDAC8 in Complex with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:26.7
occ:1.00
 O B:LEU200 2.6 29.6 1.0
OD1 B:ASP176 2.7 30.2 1.0
O B:ASP176 2.7 32.0 1.0
O B:ASP178 2.7 26.5 1.0
O B:HIS180 2.8 26.9 1.0
OG B:SER199 3.1 25.1 1.0
N B:ASP178 3.3 32.8 1.0
C B:ASP176 3.3 32.4 1.0
CG B:ASP176 3.4 33.8 1.0
C B:ASP178 3.5 27.9 1.0
C B:LEU200 3.6 28.3 1.0
CB B:ASP176 3.7 34.0 1.0
CA B:ASP178 3.7 26.1 1.0
CB B:HIS201 3.8 28.3 1.0
CB B:ASP178 3.8 27.8 1.0
C B:HIS180 3.9 23.3 1.0
C B:LEU177 3.9 33.0 1.0
N B:LEU177 3.9 27.8 1.0
N B:LEU200 4.0 29.3 1.0
CA B:LEU177 4.1 31.5 1.0
CA B:ASP176 4.1 33.4 1.0
CB B:SER199 4.2 32.7 1.0
ND1 B:HIS201 4.3 31.7 1.0
CA B:HIS201 4.3 27.6 1.0
N B:HIS201 4.4 27.9 1.0
OD2 B:ASP176 4.5 36.6 1.0
N B:GLY182 4.5 25.0 1.0
CA B:SER199 4.5 34.5 1.0
CA B:LEU200 4.5 31.9 1.0
C B:SER199 4.5 33.6 1.0
N B:HIS180 4.5 23.7 1.0
CA B:HIS181 4.5 27.8 1.0
CG B:HIS201 4.6 29.9 1.0
O B:HOH515 4.6 26.3 1.0
N B:HIS181 4.6 28.0 1.0
N B:LEU179 4.6 28.0 1.0
C B:LEU179 4.7 25.7 1.0
O B:LEU177 4.7 28.4 1.0
CE1 B:HIS142 4.8 27.4 1.0
CA B:HIS180 4.8 26.0 1.0
C B:HIS181 4.9 27.0 1.0

Potassium binding site 4 out of 4 in 4qa0

Go back to Potassium Binding Sites List in 4qa0
Potassium binding site 4 out of 4 in the Crystal Structure of C153F HDAC8 in Complex 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 C153F HDAC8 in Complex with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:41.1
occ:1.00
 O B:PHE189 2.6 40.5 1.0
O B:VAL195 2.7 34.7 1.0
O B:TYR225 2.8 38.3 1.0
O B:HOH665 2.8 43.3 1.0
O B:THR192 3.0 44.4 1.0
O B:HOH614 3.0 36.1 1.0
CB B:TYR225 3.6 44.0 1.0
C B:TYR225 3.6 42.1 1.0
C B:PHE189 3.7 39.8 1.0
OG B:SER226 3.8 35.0 1.0
C B:VAL195 3.9 35.6 1.0
C B:THR192 4.2 48.5 1.0
CB B:PHE189 4.2 35.7 1.0
CA B:TYR225 4.3 41.4 1.0
CA B:MET196 4.3 38.9 1.0
O B:GLY222 4.4 44.4 1.0
CA B:SER190 4.5 39.2 0.5
CA B:SER190 4.5 39.2 0.5
N B:SER226 4.5 38.8 1.0
N B:SER190 4.5 36.8 1.0
N B:MET196 4.6 32.6 1.0
N B:THR197 4.6 37.4 1.0
CA B:PHE189 4.6 35.0 1.0
CG2 B:THR192 4.6 38.3 1.0
C B:SER190 4.7 43.1 1.0
N B:THR192 4.8 43.8 1.0
O B:SER190 4.8 41.0 1.0
CB B:SER226 4.9 34.4 1.0
CG B:TYR225 4.9 48.5 1.0
CA B:SER226 4.9 38.4 1.0
CA B:GLY222 4.9 47.2 1.0
CG2 B:THR197 4.9 28.3 1.0
C B:MET196 5.0 38.6 1.0
CA B:THR192 5.0 43.8 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 11:49:17 2024

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