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Potassium in PDB 4rn1: 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: 4rn1 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) 43.11 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.051, 85.124, 95.354, 90.00, 100.21, 90.00
R / Rfree (%) 18.2 / 21.2

Other elements in 4rn1:

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 4rn1). 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: 4rn1:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4rn1

Go back to Potassium Binding Sites List in 4rn1
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:22.3
occ:1.00
 O A:ASP178 2.7 20.5 1.0
O A:LEU200 2.7 30.1 1.0
O A:HIS180 2.8 23.8 1.0
OD1 A:ASP176 2.8 28.5 1.0
O A:ASP176 2.8 25.0 1.0
OG A:SER199 3.0 28.8 1.0
CG A:ASP176 3.4 37.1 1.0
C A:ASP176 3.5 23.7 1.0
N A:ASP178 3.5 22.3 1.0
C A:ASP178 3.5 24.7 1.0
C A:LEU200 3.6 23.4 1.0
C A:HIS180 3.8 25.1 1.0
CB A:ASP176 3.8 28.1 1.0
CB A:HIS201 3.8 17.7 1.0
CA A:ASP178 3.8 23.8 1.0
N A:LEU200 3.9 21.9 1.0
CB A:ASP178 4.0 21.2 1.0
C A:LEU177 4.0 25.1 1.0
N A:LEU177 4.1 25.6 1.0
CB A:SER199 4.2 24.8 1.0
CA A:ASP176 4.2 29.2 1.0
CA A:LEU177 4.3 22.4 1.0
ND1 A:HIS201 4.3 21.6 1.0
CA A:HIS201 4.3 26.3 1.0
N A:HIS201 4.3 23.2 1.0
OD2 A:ASP176 4.4 33.9 1.0
CA A:LEU200 4.4 24.4 1.0
N A:GLY182 4.4 24.6 1.0
CA A:HIS181 4.4 22.8 1.0
CA A:SER199 4.4 28.9 1.0
C A:SER199 4.4 26.8 1.0
N A:HIS181 4.5 23.1 1.0
N A:HIS180 4.5 20.9 1.0
O A:HOH507 4.5 23.2 1.0
CG A:HIS201 4.5 25.2 1.0
N A:LEU179 4.7 22.6 1.0
C A:LEU179 4.7 27.1 1.0
CA A:HIS180 4.7 25.2 1.0
C A:HIS181 4.8 25.6 1.0
O A:LEU177 4.8 22.8 1.0
CE1 A:HIS142 4.9 28.4 1.0

Potassium binding site 2 out of 4 in 4rn1

Go back to Potassium Binding Sites List in 4rn1
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:30.2
occ:1.00
 O A:VAL195 2.6 29.8 1.0
O A:PHE189 2.6 27.1 1.0
O A:HOH501 2.8 26.9 1.0
O A:HOH503 2.9 27.4 1.0
O A:THR192 3.0 26.4 1.0
O A:TYR225 3.1 31.4 1.0
C A:PHE189 3.6 24.2 1.0
CB A:TYR225 3.7 25.9 1.0
C A:TYR225 3.8 28.2 1.0
OG A:SER226 3.8 30.9 1.0
C A:VAL195 3.8 29.6 1.0
C A:THR192 4.1 31.2 1.0
CB A:PHE189 4.1 29.6 1.0
CG2 A:THR192 4.3 24.2 0.5
CA A:TYR225 4.4 29.5 1.0
CA A:MET196 4.4 22.1 1.0
N A:SER190 4.4 28.7 1.0
CA A:SER190 4.4 30.5 1.0
O A:GLY222 4.5 31.1 1.0
CA A:PHE189 4.5 28.9 1.0
C A:SER190 4.6 34.1 1.0
N A:SER226 4.6 31.7 1.0
N A:THR192 4.6 28.2 1.0
O A:SER190 4.6 31.9 1.0
N A:MET196 4.6 26.2 1.0
N A:THR197 4.7 20.3 1.0
CA A:GLY222 4.8 29.1 1.0
CA A:THR192 4.8 29.8 0.5
CA A:THR192 4.9 29.8 0.5
CA A:VAL195 4.9 27.4 1.0
OG1 A:THR197 4.9 38.5 1.0
CA A:SER226 5.0 25.0 1.0
CB A:SER226 5.0 23.5 1.0

Potassium binding site 3 out of 4 in 4rn1

Go back to Potassium Binding Sites List in 4rn1
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:23.3
occ:1.00
 O B:ASP178 2.7 23.2 1.0
O B:LEU200 2.7 30.7 1.0
OD1 B:ASP176 2.8 25.7 1.0
O B:HIS180 2.8 20.0 1.0
O B:ASP176 2.9 27.1 1.0
OG B:SER199 2.9 26.1 1.0
CG B:ASP176 3.4 28.2 1.0
N B:ASP178 3.4 29.8 1.0
C B:ASP176 3.5 26.4 1.0
C B:ASP178 3.5 28.6 1.0
C B:LEU200 3.6 27.8 1.0
CB B:HIS201 3.7 24.2 1.0
C B:HIS180 3.7 27.7 1.0
CB B:ASP176 3.7 32.6 1.0
CA B:ASP178 3.8 26.7 1.0
CB B:ASP178 4.0 25.0 1.0
N B:LEU200 4.0 29.9 1.0
C B:LEU177 4.0 27.8 1.0
N B:LEU177 4.1 22.4 1.0
CB B:SER199 4.1 29.1 1.0
CA B:LEU177 4.2 20.7 1.0
CA B:ASP176 4.2 26.2 1.0
CA B:HIS201 4.3 27.1 1.0
N B:HIS201 4.3 22.9 1.0
CA B:HIS181 4.3 23.5 1.0
ND1 B:HIS201 4.4 28.0 1.0
OD2 B:ASP176 4.4 36.1 1.0
N B:GLY182 4.4 27.2 1.0
N B:HIS181 4.4 24.2 1.0
CA B:SER199 4.4 29.3 1.0
C B:SER199 4.4 27.3 1.0
N B:HIS180 4.4 20.4 1.0
CA B:LEU200 4.5 26.9 1.0
CG B:HIS201 4.5 21.8 1.0
O B:HOH505 4.5 26.2 1.0
N B:LEU179 4.7 26.1 1.0
C B:LEU179 4.7 32.0 1.0
CE1 B:HIS142 4.7 25.5 1.0
CA B:HIS180 4.7 27.6 1.0
C B:HIS181 4.7 26.4 1.0
O B:LEU177 4.8 22.0 1.0

Potassium binding site 4 out of 4 in 4rn1

Go back to Potassium Binding Sites List in 4rn1
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:33.6
occ:1.00
 O B:PHE189 2.6 34.9 1.0
O B:VAL195 2.6 28.7 1.0
O B:HOH501 2.8 26.1 1.0
O B:HOH503 2.9 30.6 1.0
O B:THR192 2.9 43.6 1.0
O B:TYR225 3.0 40.1 1.0
C B:PHE189 3.7 33.9 1.0
C B:TYR225 3.8 41.3 1.0
CB B:TYR225 3.8 34.7 1.0
OG B:SER226 3.8 37.9 1.0
C B:VAL195 3.9 31.8 1.0
CB B:PHE189 4.1 24.2 1.0
C B:THR192 4.1 40.2 1.0
CA B:MET196 4.4 35.1 1.0
CA B:TYR225 4.4 38.5 1.0
O B:GLY222 4.5 42.4 1.0
N B:SER190 4.5 34.9 1.0
CA B:PHE189 4.5 33.0 1.0
CA B:SER190 4.5 36.2 1.0
N B:SER226 4.6 35.3 1.0
N B:THR197 4.6 27.3 1.0
N B:MET196 4.6 28.0 1.0
O B:SER190 4.6 36.8 1.0
C B:SER190 4.6 40.0 1.0
CG2 B:THR192 4.6 37.2 1.0
OG1 B:THR197 4.8 40.4 1.0
N B:THR192 4.8 41.3 1.0
CA B:VAL195 4.9 33.0 1.0
CA B:SER226 5.0 34.1 1.0
CB B:SER226 5.0 37.3 1.0
CA B:SER193 5.0 34.4 1.0
C B:MET196 5.0 34.3 1.0
N B:SER193 5.0 36.6 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: Sun Dec 13 23:48:58 2020

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