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Potassium in PDB 4rn2: Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.

Enzymatic activity of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.

All present enzymatic activity of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue., PDB code: 4rn2 was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.99 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.764, 84.712, 94.139, 90.00, 100.47, 90.00
R / Rfree (%) 18.7 / 22.4

Other elements in 4rn2:

The structure of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue. (pdb code 4rn2). 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 S39D HDAC8 in Complex with A Largazole Analogue., PDB code: 4rn2:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4rn2

Go back to Potassium Binding Sites List in 4rn2
Potassium binding site 1 out of 4 in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.


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 S39D HDAC8 in Complex with A Largazole Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:29.0
occ:1.00
 O A:ASP178 2.7 26.1 1.0
O A:LEU200 2.7 36.7 1.0
O A:HIS180 2.8 33.6 1.0
O A:ASP176 2.9 34.8 1.0
OD1 A:ASP176 3.0 35.4 1.0
OG A:SER199 3.0 27.1 1.0
N A:ASP178 3.4 36.5 1.0
CG A:ASP176 3.5 35.6 1.0
C A:ASP178 3.5 31.9 1.0
C A:ASP176 3.5 28.8 1.0
C A:LEU200 3.6 32.7 1.0
CB A:HIS201 3.7 23.5 1.0
C A:HIS180 3.7 26.0 1.0
CA A:ASP178 3.8 29.3 1.0
CB A:ASP176 3.8 37.7 1.0
CB A:ASP178 3.9 29.1 1.0
N A:LEU200 4.0 33.7 1.0
C A:LEU177 4.1 33.5 1.0
N A:LEU177 4.2 28.8 1.0
CB A:SER199 4.2 36.3 1.0
CA A:HIS201 4.2 31.6 1.0
N A:HIS201 4.3 36.9 1.0
N A:GLY182 4.3 32.4 1.0
OD2 A:ASP176 4.3 37.9 1.0
CA A:ASP176 4.3 33.0 1.0
CA A:LEU177 4.3 31.6 1.0
CA A:HIS181 4.3 32.6 1.0
ND1 A:HIS201 4.4 36.0 1.0
N A:HIS181 4.4 30.7 1.0
CA A:LEU200 4.5 33.5 1.0
C A:SER199 4.5 42.7 1.0
N A:HIS180 4.5 24.7 1.0
CA A:SER199 4.5 37.3 1.0
CG A:HIS201 4.5 34.1 1.0
O A:HOH507 4.6 27.8 1.0
N A:LEU179 4.6 31.3 1.0
C A:LEU179 4.7 30.4 1.0
CE1 A:HIS142 4.7 35.4 1.0
C A:HIS181 4.7 38.4 1.0
CA A:HIS180 4.7 27.7 1.0
O A:LEU177 4.9 39.0 1.0
O A:LEU179 4.9 31.1 1.0

Potassium binding site 2 out of 4 in 4rn2

Go back to Potassium Binding Sites List in 4rn2
Potassium binding site 2 out of 4 in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.


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 S39D HDAC8 in Complex with A Largazole Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:40.6
occ:1.00
 O A:VAL195 2.7 39.6 1.0
O A:PHE189 2.7 38.7 1.0
O A:HOH580 2.8 47.1 1.0
O A:HOH592 2.9 38.5 1.0
O A:TYR225 2.9 48.3 1.0
O A:THR192 3.1 40.3 1.0
CB A:TYR225 3.7 45.0 1.0
C A:PHE189 3.7 37.5 1.0
C A:TYR225 3.7 47.8 1.0
OG A:SER226 3.7 46.0 1.0
C A:VAL195 3.9 36.1 1.0
CB A:PHE189 4.1 28.1 1.0
C A:THR192 4.3 40.8 1.0
CA A:MET196 4.3 38.5 1.0
CA A:TYR225 4.3 45.8 1.0
O A:GLY222 4.3 57.0 1.0
CA A:SER190 4.5 38.0 1.0
N A:SER190 4.5 33.1 1.0
CG2 A:THR192 4.5 36.2 1.0
N A:SER226 4.5 34.3 1.0
N A:MET196 4.6 26.8 1.0
N A:THR197 4.6 37.4 1.0
CA A:PHE189 4.6 36.8 1.0
C A:SER190 4.7 44.4 1.0
N A:THR192 4.7 42.1 1.0
O A:SER190 4.8 48.9 1.0
OG1 A:THR197 4.9 39.4 1.0
CB A:SER226 4.9 40.4 1.0
C A:MET196 4.9 38.4 1.0
CG A:TYR225 4.9 45.1 1.0
CA A:SER226 4.9 41.0 1.0
CA A:GLY222 5.0 48.9 1.0
CA A:VAL195 5.0 37.5 1.0

Potassium binding site 3 out of 4 in 4rn2

Go back to Potassium Binding Sites List in 4rn2
Potassium binding site 3 out of 4 in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.


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 S39D HDAC8 in Complex with A Largazole Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:27.6
occ:1.00
 O B:LEU200 2.7 29.5 1.0
OD1 B:ASP176 2.8 33.1 1.0
O B:ASP178 2.8 28.0 1.0
O B:HIS180 2.8 27.1 1.0
O B:ASP176 2.8 34.6 1.0
OG B:SER199 2.9 28.1 1.0
N B:ASP178 3.5 27.1 1.0
CG B:ASP176 3.5 36.7 1.0
C B:ASP176 3.5 33.4 1.0
C B:ASP178 3.5 22.4 1.0
C B:LEU200 3.6 28.8 1.0
CB B:HIS201 3.7 31.9 1.0
CB B:ASP176 3.8 33.1 1.0
C B:HIS180 3.8 27.8 1.0
CA B:ASP178 3.8 23.1 1.0
N B:LEU200 3.9 27.3 1.0
CB B:ASP178 4.0 27.2 1.0
C B:LEU177 4.1 26.0 1.0
CB B:SER199 4.1 29.6 1.0
N B:LEU177 4.2 30.9 1.0
CA B:HIS201 4.2 24.2 1.0
CA B:ASP176 4.3 30.5 1.0
N B:HIS201 4.3 27.8 1.0
ND1 B:HIS201 4.3 28.7 1.0
CA B:LEU177 4.4 30.2 1.0
CA B:SER199 4.4 28.7 1.0
OD2 B:ASP176 4.4 31.8 1.0
N B:GLY182 4.4 28.9 1.0
C B:SER199 4.4 30.2 1.0
CA B:LEU200 4.4 28.7 1.0
CA B:HIS181 4.4 27.7 1.0
CG B:HIS201 4.5 29.4 1.0
O B:HOH503 4.5 23.9 1.0
N B:HIS181 4.5 28.3 1.0
N B:HIS180 4.5 22.9 1.0
N B:LEU179 4.6 29.9 1.0
CE1 B:HIS142 4.7 32.2 1.0
C B:LEU179 4.7 29.5 1.0
C B:HIS181 4.8 31.2 1.0
CA B:HIS180 4.8 22.9 1.0
O B:LEU179 4.9 26.3 1.0
O B:LEU177 4.9 29.1 1.0

Potassium binding site 4 out of 4 in 4rn2

Go back to Potassium Binding Sites List in 4rn2
Potassium binding site 4 out of 4 in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.


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 S39D HDAC8 in Complex with A Largazole Analogue. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:32.4
occ:1.00
 O B:VAL195 2.6 28.7 1.0
O B:PHE189 2.6 28.1 1.0
O B:HOH501 2.7 25.4 1.0
O B:TYR225 2.8 37.2 1.0
O B:THR192 2.9 35.5 1.0
O B:HOH505 3.0 30.0 1.0
CB B:TYR225 3.7 33.6 1.0
C B:PHE189 3.7 31.9 1.0
C B:TYR225 3.7 37.8 1.0
OG B:SER226 3.8 33.6 1.0
C B:VAL195 3.8 31.3 1.0
C B:THR192 4.1 36.4 1.0
CB B:PHE189 4.2 26.7 1.0
CA B:TYR225 4.3 37.9 1.0
CG2 B:THR192 4.4 29.3 1.0
CA B:MET196 4.4 26.3 1.0
O B:GLY222 4.4 43.2 1.0
CA B:SER190 4.4 37.0 1.0
N B:SER190 4.5 27.9 1.0
N B:MET196 4.6 24.7 1.0
N B:SER226 4.6 31.5 1.0
CA B:PHE189 4.6 26.9 1.0
N B:THR192 4.6 27.9 1.0
N B:THR197 4.7 30.9 1.0
C B:SER190 4.7 36.1 1.0
CA B:GLY222 4.7 34.5 1.0
CA B:VAL195 4.9 26.0 1.0
CA B:THR192 4.9 31.5 1.0
CG2 B:THR197 4.9 33.1 1.0
CG B:TYR225 4.9 35.5 1.0
CB B:SER226 4.9 34.0 1.0
O B:SER190 4.9 43.5 1.0
CA B:SER226 5.0 35.7 1.0
C B:MET196 5.0 32.2 1.0

Reference:

C.Decroos, D.J.Clausen, B.E.Haines, O.Wiest, R.M.Williams, D.W.Christianson. Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25793284
DOI: 10.1021/ACS.BIOCHEM.5B00010
Page generated: Mon Aug 12 12:02:34 2024

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