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Potassium in PDB 6hsk: Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat

Enzymatic activity of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat

All present enzymatic activity of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat, PDB code: 6hsk was solved by M.Marek, T.B.Shaik, E.Ramos-Morales, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.47 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 106.390, 106.390, 82.030, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 18.9

Other elements in 6hsk:

The structure of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat (pdb code 6hsk). 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 A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat, PDB code: 6hsk:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6hsk

Go back to Potassium Binding Sites List in 6hsk
Potassium binding site 1 out of 4 in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat


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 A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:29.4
occ:1.00
 O A:LEU200 2.6 25.4 1.0
O A:ASP178 2.7 26.2 1.0
OD1 A:ASP176 2.7 25.3 1.0
O A:ASP176 2.7 25.4 1.0
O A:HIS180 2.8 26.7 1.0
OG A:SER199 2.9 26.4 1.0
C A:ASP176 3.4 26.5 1.0
CG A:ASP176 3.4 29.0 1.0
N A:ASP178 3.5 29.4 1.0
C A:ASP178 3.5 30.1 1.0
C A:LEU200 3.6 28.5 1.0
C A:HIS180 3.7 29.6 1.0
CB A:HIS201 3.8 24.3 1.0
CB A:ASP176 3.8 24.9 1.0
N A:LEU200 3.8 30.3 1.0
CA A:ASP178 3.9 25.9 1.0
C A:LEU177 3.9 27.5 1.0
CB A:ASP178 4.0 24.2 1.0
N A:LEU177 4.0 25.9 1.0
CA A:LEU177 4.1 27.4 1.0
CB A:SER199 4.1 26.0 1.0
CA A:ASP176 4.2 27.2 1.0
N A:GLY182 4.3 29.3 1.0
CA A:HIS201 4.3 31.0 1.0
CA A:SER199 4.3 20.2 1.0
OD2 A:ASP176 4.3 28.4 1.0
ND1 A:HIS201 4.3 30.4 1.0
CA A:LEU200 4.4 30.1 1.0
CA A:HIS181 4.4 30.1 1.0
N A:HIS181 4.4 26.7 1.0
O A:HOH571 4.4 29.9 1.0
N A:HIS180 4.4 28.3 1.0
N A:HIS201 4.4 28.2 1.0
C A:SER199 4.4 30.6 1.0
CG A:HIS201 4.5 29.6 1.0
O A:LEU177 4.6 25.6 1.0
C A:LEU179 4.6 32.0 1.0
C A:HIS181 4.7 30.3 1.0
CA A:HIS180 4.7 30.4 1.0
N A:LEU179 4.7 31.3 1.0
O A:LEU179 5.0 29.3 1.0

Potassium binding site 2 out of 4 in 6hsk

Go back to Potassium Binding Sites List in 6hsk
Potassium binding site 2 out of 4 in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat


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 A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:47.0
occ:1.00
 O A:VAL195 2.4 33.8 1.0
O A:PHE189 2.5 26.4 1.0
O A:HOH512 2.6 30.9 1.0
O A:THR192 2.7 29.2 1.0
O A:HOH611 2.8 35.1 1.0
O A:TYR225 3.2 34.4 1.0
C A:PHE189 3.5 30.9 1.0
C A:VAL195 3.6 30.9 1.0
C A:THR192 3.9 32.8 1.0
CB A:TYR225 3.9 27.4 1.0
C A:TYR225 3.9 34.7 1.0
CB A:PHE189 4.0 28.6 1.0
OG A:SER226 4.0 36.5 1.0
CG2 A:THR192 4.2 26.4 1.0
N A:THR192 4.3 29.6 1.0
CA A:MET196 4.3 30.4 1.0
O A:SER190 4.4 39.6 1.0
CA A:PHE189 4.4 27.4 1.0
N A:SER190 4.4 31.3 1.0
CA A:SER190 4.4 39.4 1.0
C A:SER190 4.4 37.7 1.0
N A:MET196 4.4 29.1 1.0
CA A:TYR225 4.5 31.2 1.0
CA A:THR192 4.6 28.3 1.0
CA A:VAL195 4.6 31.5 1.0
O A:GLY222 4.6 32.4 1.0
N A:SER226 4.7 33.3 1.0
N A:THR197 4.8 33.1 1.0
N A:VAL195 4.8 28.2 1.0
CA A:GLY222 4.8 31.2 1.0
CB A:VAL195 4.8 24.9 1.0
N A:SER193 4.9 31.6 1.0
C A:MET196 5.0 30.6 1.0

Potassium binding site 3 out of 4 in 6hsk

Go back to Potassium Binding Sites List in 6hsk
Potassium binding site 3 out of 4 in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat


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 A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:28.6
occ:1.00
 OD1 B:ASP176 2.6 28.6 1.0
O B:LEU200 2.6 30.8 1.0
O B:ASP178 2.7 28.7 1.0
O B:HIS180 2.7 28.2 1.0
O B:ASP176 2.8 29.6 1.0
OG B:SER199 2.9 27.9 1.0
CG B:ASP176 3.4 28.7 1.0
C B:ASP176 3.5 26.1 1.0
N B:ASP178 3.5 28.9 1.0
C B:ASP178 3.5 27.0 1.0
C B:LEU200 3.6 34.7 1.0
C B:HIS180 3.8 26.8 1.0
CB B:HIS201 3.8 21.2 1.0
CB B:ASP176 3.8 23.3 1.0
CA B:ASP178 3.8 29.3 1.0
CB B:ASP178 3.9 22.0 1.0
N B:LEU200 3.9 30.5 1.0
C B:LEU177 3.9 29.5 1.0
N B:LEU177 4.1 29.5 1.0
CB B:SER199 4.1 29.8 1.0
CA B:LEU177 4.2 25.7 1.0
ND1 B:HIS201 4.3 33.7 1.0
CA B:ASP176 4.3 25.8 1.0
CA B:HIS201 4.3 29.1 1.0
OD2 B:ASP176 4.3 29.3 1.0
N B:HIS201 4.4 33.1 1.0
CA B:SER199 4.4 29.6 1.0
N B:HIS180 4.4 24.8 1.0
N B:GLY182 4.4 30.4 1.0
CA B:LEU200 4.4 32.1 1.0
O B:HOH553 4.4 23.0 1.0
CA B:HIS181 4.4 29.6 1.0
C B:SER199 4.5 32.7 1.0
N B:HIS181 4.5 24.8 1.0
CG B:HIS201 4.5 29.3 1.0
C B:LEU179 4.6 33.3 1.0
O B:LEU177 4.7 30.1 1.0
N B:LEU179 4.7 25.7 1.0
CA B:HIS180 4.7 23.8 1.0
C B:HIS181 4.7 29.9 1.0
O B:LEU179 4.9 28.2 1.0
CE1 B:HIS142 4.9 32.9 1.0

Potassium binding site 4 out of 4 in 6hsk

Go back to Potassium Binding Sites List in 6hsk
Potassium binding site 4 out of 4 in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat


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 A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:51.1
occ:1.00
 O B:PHE189 2.4 28.9 1.0
O B:VAL195 2.5 30.6 1.0
O B:HOH518 2.5 28.9 1.0
O B:THR192 2.7 38.0 1.0
O B:HOH621 2.7 37.9 1.0
O B:TYR225 3.3 31.6 1.0
C B:PHE189 3.5 36.7 1.0
C B:VAL195 3.7 32.8 1.0
CB B:TYR225 3.7 37.9 1.0
C B:THR192 3.9 36.0 1.0
C B:TYR225 3.9 35.8 1.0
CB B:PHE189 4.0 30.8 1.0
OG B:SER226 4.2 40.1 1.0
CG2 B:THR192 4.2 30.5 1.0
N B:THR192 4.3 30.3 1.0
N B:SER190 4.3 32.7 1.0
CA B:MET196 4.3 33.8 1.0
CA B:PHE189 4.3 31.7 1.0
O B:SER190 4.3 34.8 1.0
CA B:SER190 4.4 33.4 1.0
C B:SER190 4.4 39.6 1.0
CA B:TYR225 4.4 31.5 1.0
N B:MET196 4.5 29.2 1.0
O B:GLY222 4.6 32.5 1.0
CA B:THR192 4.6 30.0 1.0
N B:SER226 4.6 30.6 1.0
CA B:VAL195 4.7 31.7 1.0
N B:THR197 4.7 29.4 1.0
CA B:GLY222 4.7 35.7 1.0
N B:VAL195 4.8 31.4 1.0
CB B:VAL195 4.9 29.9 1.0
N B:SER193 4.9 31.3 1.0
C B:MET196 5.0 32.5 1.0

Reference:

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087
Page generated: Mon Aug 12 16:24:14 2024

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