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Potassium in PDB 4qa3: Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)

Enzymatic activity of Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)

All present enzymatic activity of Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa):
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa), PDB code: 4qa3 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) 46.90 / 2.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.186, 83.094, 94.297, 90.00, 95.94, 90.00
R / Rfree (%) 17.8 / 23.4

Other elements in 4qa3:

The structure of Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa) (pdb code 4qa3). 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 T311M HDAC8 in Complex with Trichostatin A (Tsa), PDB code: 4qa3:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4qa3

Go back to Potassium Binding Sites List in 4qa3
Potassium binding site 1 out of 4 in the Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)


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 T311M HDAC8 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:23.2
occ:1.00
O A:ASP178 2.8 29.6 1.0
O A:LEU200 2.8 28.3 1.0
OD1 A:ASP176 2.8 27.9 1.0
O A:HIS180 2.9 28.3 1.0
O A:ASP176 3.0 27.3 1.0
OG A:SER199 3.1 31.2 1.0
N A:ASP178 3.4 28.2 1.0
CG A:ASP176 3.4 28.1 1.0
C A:ASP176 3.5 27.8 1.0
C A:ASP178 3.5 27.6 1.0
C A:LEU200 3.6 26.1 1.0
CB A:HIS201 3.7 27.6 1.0
CB A:ASP176 3.7 25.3 1.0
C A:HIS180 3.8 29.3 1.0
CA A:ASP178 3.8 27.9 1.0
N A:LEU200 3.9 27.0 1.0
CB A:ASP178 4.0 29.7 1.0
C A:LEU177 4.0 30.6 1.0
N A:LEU177 4.0 29.6 1.0
CA A:LEU177 4.2 27.0 1.0
CA A:HIS201 4.2 27.9 1.0
CA A:ASP176 4.2 28.2 1.0
CB A:SER199 4.2 26.9 1.0
N A:HIS201 4.3 26.4 1.0
OD2 A:ASP176 4.3 29.9 1.0
CA A:HIS181 4.3 26.0 1.0
C A:SER199 4.4 29.4 1.0
ND1 A:HIS201 4.4 26.7 1.0
CA A:LEU200 4.4 25.7 1.0
CA A:SER199 4.4 24.3 1.0
N A:HIS181 4.4 27.7 1.0
N A:GLY182 4.4 28.0 1.0
CG A:HIS201 4.5 26.3 1.0
N A:HIS180 4.6 29.2 1.0
O A:HOH602 4.6 25.5 1.0
N A:LEU179 4.7 27.6 1.0
C A:LEU179 4.7 29.0 1.0
C A:HIS181 4.8 30.1 1.0
CA A:HIS180 4.8 31.2 1.0
CE1 A:HIS142 4.8 29.7 1.0
O A:LEU177 4.9 34.5 1.0
O A:LEU179 5.0 28.8 1.0

Potassium binding site 2 out of 4 in 4qa3

Go back to Potassium Binding Sites List in 4qa3
Potassium binding site 2 out of 4 in the Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)


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 T311M HDAC8 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:27.6
occ:1.00
O A:PHE189 2.7 33.0 1.0
O A:VAL195 2.7 29.5 1.0
O A:HOH614 2.8 33.8 1.0
O A:HOH613 2.8 31.6 1.0
O A:THR192 3.0 33.4 1.0
O A:TYR225 3.0 26.3 1.0
C A:TYR225 3.6 29.2 1.0
C A:PHE189 3.7 31.6 1.0
CB A:TYR225 3.7 30.5 1.0
OG A:SER226 3.7 30.6 1.0
C A:VAL195 3.9 31.7 1.0
CB A:PHE189 4.2 34.8 1.0
C A:THR192 4.2 31.6 1.0
CA A:TYR225 4.3 30.8 1.0
N A:SER226 4.3 29.4 1.0
CA A:MET196 4.3 29.4 1.0
O A:GLY222 4.4 31.7 1.0
CA A:SER190 4.4 29.3 1.0
O A:SER190 4.5 31.3 1.0
N A:SER190 4.5 31.8 1.0
N A:THR197 4.5 26.7 1.0
C A:SER190 4.6 29.9 1.0
N A:MET196 4.6 31.5 1.0
CA A:PHE189 4.6 31.0 1.0
OG1 A:THR197 4.7 28.2 1.0
CA A:SER226 4.7 27.1 1.0
CG2 A:THR192 4.7 29.8 1.0
N A:THR192 4.8 29.2 1.0
CB A:SER226 4.8 27.2 1.0
C A:MET196 4.9 30.7 1.0
CA A:GLY222 5.0 30.6 1.0

Potassium binding site 3 out of 4 in 4qa3

Go back to Potassium Binding Sites List in 4qa3
Potassium binding site 3 out of 4 in the Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)


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 T311M HDAC8 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:41.5
occ:1.00
O B:ASP176 2.8 42.5 1.0
O B:HIS180 2.8 34.2 1.0
OD1 B:ASP176 2.9 42.1 1.0
O B:LEU200 3.0 44.5 1.0
O B:ASP178 3.1 37.1 1.0
OG B:SER199 3.2 43.3 1.0
CG B:ASP176 3.3 42.5 1.0
N B:ASP178 3.3 38.4 1.0
C B:ASP176 3.3 41.1 1.0
CB B:ASP176 3.6 38.6 1.0
C B:LEU200 3.7 41.3 1.0
C B:ASP178 3.8 37.3 1.0
CB B:HIS201 3.8 40.2 1.0
CA B:ASP178 3.9 36.0 1.0
N B:LEU200 3.9 47.3 1.0
CB B:ASP178 3.9 41.6 1.0
N B:LEU177 4.0 41.3 1.0
C B:HIS180 4.0 39.0 1.0
C B:LEU177 4.0 41.1 1.0
CA B:ASP176 4.1 38.0 1.0
CB B:SER199 4.2 42.4 1.0
OD2 B:ASP176 4.2 44.1 1.0
CA B:LEU177 4.2 39.0 1.0
CA B:SER199 4.3 40.0 1.0
C B:SER199 4.3 46.0 1.0
N B:HIS201 4.3 42.9 1.0
N B:GLY182 4.3 37.9 1.0
CA B:HIS201 4.4 41.4 1.0
CA B:HIS181 4.4 41.8 1.0
ND1 B:HIS201 4.4 46.2 1.0
CA B:LEU200 4.4 42.9 1.0
CG B:HIS201 4.6 47.0 1.0
N B:HIS181 4.6 42.9 1.0
N B:HIS180 4.8 41.2 1.0
C B:HIS181 4.8 40.1 1.0
O B:LEU177 4.9 44.1 1.0
N B:LEU179 4.9 41.3 1.0
CE1 B:HIS142 4.9 41.7 1.0

Potassium binding site 4 out of 4 in 4qa3

Go back to Potassium Binding Sites List in 4qa3
Potassium binding site 4 out of 4 in the Crystal Structure of T311M HDAC8 in Complex with Trichostatin A (Tsa)


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 T311M HDAC8 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:53.8
occ:1.00
O B:PHE189 2.7 54.9 1.0
O B:VAL195 2.8 46.3 1.0
O B:TYR225 2.9 45.2 1.0
O B:HOH506 3.0 56.7 1.0
OG B:SER226 3.0 51.2 1.0
O B:THR192 3.0 55.9 1.0
O B:HOH505 3.2 53.0 1.0
C B:TYR225 3.4 50.7 1.0
CB B:TYR225 3.5 55.6 1.0
C B:PHE189 3.8 53.4 1.0
C B:VAL195 4.0 48.2 1.0
CA B:TYR225 4.1 59.0 1.0
O B:GLY222 4.2 65.0 1.0
N B:SER226 4.2 53.2 1.0
C B:THR192 4.2 56.3 1.0
CB B:SER226 4.3 47.4 1.0
CA B:MET196 4.4 47.7 1.0
CB B:PHE189 4.4 50.1 1.0
CA B:SER190 4.5 50.2 1.0
N B:THR197 4.5 48.1 1.0
CA B:SER226 4.5 51.4 1.0
N B:SER190 4.6 51.5 1.0
OG1 B:THR197 4.6 42.5 1.0
N B:MET196 4.6 44.7 1.0
N B:THR192 4.7 53.8 1.0
C B:SER190 4.7 57.1 1.0
CG B:TYR225 4.8 56.7 1.0
CA B:PHE189 4.8 50.2 1.0
O B:SER190 4.8 59.6 1.0
C B:MET196 4.9 48.1 1.0
CA B:GLY222 4.9 57.1 1.0
CG2 B:THR197 4.9 42.2 1.0
CA B:THR192 4.9 52.2 1.0
N B:TYR225 5.0 58.7 1.0
C B:GLY222 5.0 59.3 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: Sun Dec 13 23:48:18 2020

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