Atomistry » Potassium » PDB 4qxg-4tog » 4rn0
Atomistry »
  Potassium »
    PDB 4qxg-4tog »
      4rn0 »

Potassium in PDB 4rn0: 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: 4rn0 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) 42.91 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.921, 85.006, 94.665, 90.00, 100.33, 90.00
R / Rfree (%) 13.7 / 16.2

Other elements in 4rn0:

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 4rn0). 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: 4rn0:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4rn0

Go back to Potassium Binding Sites List in 4rn0
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:K503

b:10.5
occ:1.00
 OD1 A:ASP176 2.7 12.1 1.0
O A:LEU200 2.7 10.9 1.0
O A:ASP178 2.7 11.0 1.0
O A:HIS180 2.8 9.5 1.0
O A:ASP176 2.8 11.4 1.0
OG A:SER199 2.8 11.6 1.0
CG A:ASP176 3.4 11.6 1.0
C A:ASP176 3.5 10.8 1.0
N A:ASP178 3.5 9.9 1.0
C A:ASP178 3.6 8.8 1.0
C A:LEU200 3.6 9.7 1.0
C A:HIS180 3.7 9.6 1.0
CB A:HIS201 3.8 11.5 1.0
CA A:ASP178 3.9 10.3 1.0
N A:LEU200 3.9 9.3 1.0
CB A:ASP176 3.9 9.7 1.0
CB A:ASP178 3.9 9.3 1.0
C A:LEU177 4.0 8.5 1.0
CB A:SER199 4.1 12.0 1.0
N A:LEU177 4.1 10.5 1.0
CA A:LEU177 4.2 10.2 1.0
ND1 A:HIS201 4.3 12.2 1.0
CA A:ASP176 4.3 9.4 1.0
OD2 A:ASP176 4.3 13.4 1.0
N A:GLY182 4.3 12.4 1.0
CA A:SER199 4.3 9.7 1.0
N A:HIS180 4.4 9.7 1.0
CA A:HIS201 4.4 8.9 1.0
CA A:HIS181 4.4 8.7 1.0
N A:HIS201 4.4 9.7 1.0
C A:SER199 4.4 10.8 1.0
N A:HIS181 4.4 9.4 1.0
CA A:LEU200 4.5 9.2 1.0
O A:HOH605 4.5 11.7 1.0
CG A:HIS201 4.5 9.6 1.0
C A:LEU179 4.6 11.2 1.0
CA A:HIS180 4.7 9.3 1.0
C A:HIS181 4.7 11.3 1.0
N A:LEU179 4.7 8.6 1.0
O A:LEU177 4.8 10.5 1.0
CE1 A:HIS142 4.9 12.4 1.0
O A:LEU179 5.0 10.5 1.0

Potassium binding site 2 out of 4 in 4rn0

Go back to Potassium Binding Sites List in 4rn0
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:K504

b:13.7
occ:1.00
 O A:VAL195 2.6 14.9 1.0
O A:HOH601 2.7 15.4 1.0
O A:PHE189 2.7 14.9 1.0
O A:THR192 2.8 17.3 1.0
O A:HOH610 2.8 17.3 1.0
O A:TYR225 3.0 14.7 1.0
CB A:TYR225 3.6 14.6 1.0
C A:PHE189 3.6 14.6 1.0
C A:TYR225 3.7 14.7 1.0
C A:VAL195 3.8 14.8 1.0
C A:THR192 4.0 16.8 1.0
CB A:PHE189 4.1 13.0 1.0
OG A:SER226 4.2 17.8 1.0
CA A:TYR225 4.3 13.2 1.0
O A:SER190 4.4 17.4 1.0
CA A:SER190 4.4 14.8 1.0
CA A:MET196 4.4 12.5 1.0
CG2 A:THR192 4.4 15.3 1.0
C A:SER190 4.4 17.4 1.0
N A:SER190 4.4 14.8 1.0
N A:THR192 4.5 15.6 1.0
N A:SER226 4.5 12.4 1.0
CA A:PHE189 4.5 11.8 1.0
N A:MET196 4.6 12.4 1.0
O A:GLY222 4.6 15.6 1.0
N A:THR197 4.7 11.6 1.0
CA A:THR192 4.8 14.8 1.0
CA A:VAL195 4.8 10.9 1.0
CA A:GLY222 4.9 15.0 1.0
CG A:TYR225 4.9 15.8 1.0
OG1 A:THR197 4.9 16.0 1.0
CB A:VAL195 4.9 12.7 1.0
N A:VAL195 5.0 13.1 1.0
C A:MET196 5.0 11.8 1.0

Potassium binding site 3 out of 4 in 4rn0

Go back to Potassium Binding Sites List in 4rn0
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:K503

b:12.3
occ:1.00
 OD1 B:ASP176 2.6 13.4 1.0
O B:ASP178 2.7 11.3 1.0
O B:LEU200 2.7 12.1 1.0
O B:HIS180 2.8 12.8 1.0
O B:ASP176 2.8 12.0 1.0
OG B:SER199 2.9 15.2 1.0
CG B:ASP176 3.4 15.4 1.0
C B:ASP176 3.4 11.8 1.0
N B:ASP178 3.5 13.0 1.0
C B:ASP178 3.6 11.8 1.0
C B:LEU200 3.7 12.5 1.0
C B:HIS180 3.7 12.7 1.0
CB B:HIS201 3.9 12.3 1.0
CA B:ASP178 3.9 10.3 1.0
CB B:ASP176 3.9 11.4 1.0
N B:LEU200 4.0 11.7 1.0
C B:LEU177 4.0 11.6 1.0
CB B:ASP178 4.0 10.2 1.0
CB B:SER199 4.0 13.8 1.0
N B:LEU177 4.1 10.3 1.0
CA B:LEU177 4.2 10.7 1.0
ND1 B:HIS201 4.3 13.3 1.0
CA B:ASP176 4.3 12.4 1.0
OD2 B:ASP176 4.3 14.6 1.0
N B:GLY182 4.3 11.2 1.0
CA B:SER199 4.4 13.4 1.0
CA B:HIS201 4.4 11.1 1.0
CA B:HIS181 4.4 10.0 1.0
N B:HIS180 4.4 10.2 1.0
N B:HIS201 4.5 11.4 1.0
N B:HIS181 4.5 10.7 1.0
C B:SER199 4.5 13.7 1.0
CA B:LEU200 4.5 12.3 1.0
CG B:HIS201 4.5 11.8 1.0
O B:HOH606 4.6 14.6 1.0
C B:LEU179 4.6 11.5 1.0
C B:HIS181 4.7 11.3 1.0
CA B:HIS180 4.7 11.0 1.0
N B:LEU179 4.7 8.8 1.0
O B:LEU177 4.7 10.8 1.0
CE1 B:HIS142 4.8 14.0 1.0
O B:LEU179 4.9 11.7 1.0

Potassium binding site 4 out of 4 in 4rn0

Go back to Potassium Binding Sites List in 4rn0
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:K504

b:18.7
occ:1.00
 O B:PHE189 2.6 21.4 1.0
O B:VAL195 2.6 19.6 1.0
O B:THR192 2.8 22.3 1.0
O B:HOH603 2.8 19.1 1.0
O B:HOH611 2.8 20.2 1.0
O B:TYR225 3.0 19.3 1.0
C B:PHE189 3.6 20.8 1.0
CB B:TYR225 3.7 16.9 1.0
C B:TYR225 3.7 17.5 1.0
C B:VAL195 3.8 17.7 1.0
C B:THR192 4.0 26.5 1.0
CB B:PHE189 4.0 17.0 1.0
OG B:SER226 4.1 22.5 1.0
CA B:TYR225 4.3 20.1 1.0
CA B:SER190 4.4 16.9 0.6
CA B:PHE189 4.4 17.7 1.0
CA B:MET196 4.4 19.2 0.6
N B:SER190 4.4 18.2 1.0
CA B:SER190 4.5 18.3 0.4
CA B:MET196 4.5 19.2 0.4
N B:SER226 4.5 17.9 1.0
O B:SER190 4.5 23.0 1.0
C B:SER190 4.5 23.1 1.0
N B:THR192 4.5 23.4 1.0
CG2 B:THR192 4.6 26.8 1.0
N B:THR197 4.6 16.5 1.0
N B:MET196 4.6 15.6 1.0
O B:GLY222 4.6 23.5 1.0
CA B:THR192 4.8 26.0 1.0
CA B:VAL195 4.9 14.5 1.0
OG1 B:THR197 4.9 22.2 1.0
N B:SER193 5.0 23.5 1.0
CG2 B:THR197 5.0 18.2 1.0
N B:VAL195 5.0 15.0 1.0
CG B:TYR225 5.0 21.7 1.0
C B:MET196 5.0 19.2 1.0
CA B:SER226 5.0 20.7 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 12:01:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy