Atomistry » Potassium » PDB 5cbv-5dea » 5d1c
Atomistry »
  Potassium »
    PDB 5cbv-5dea »
      5d1c »

Potassium in PDB 5d1c: Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

Enzymatic activity of Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5d1c was solved by C.Decroos, N.H.Christianson, L.E.Gullett, C.M.Bowman, 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) 44.35 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.031, 97.936, 104.656, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 16.7

Other elements in 5d1c:

The structure of Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5d1c). 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 D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5d1c:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5d1c

Go back to Potassium Binding Sites List in 5d1c
Potassium binding site 1 out of 4 in the Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:10.4
occ:1.00
 OD1 A:ASP176 2.7 11.1 1.0
O A:LEU200 2.7 10.9 1.0
O A:ASP178 2.7 10.8 1.0
O A:HIS180 2.8 10.1 1.0
O A:ASP176 2.8 11.1 1.0
OG A:SER199 2.9 13.0 1.0
CG A:ASP176 3.4 12.4 1.0
C A:ASP176 3.5 10.7 1.0
N A:ASP178 3.5 10.4 1.0
C A:ASP178 3.6 9.0 1.0
C A:LEU200 3.7 10.8 1.0
C A:HIS180 3.8 9.4 1.0
CB A:HIS201 3.8 10.3 1.0
CA A:ASP178 3.9 9.8 1.0
N A:LEU200 3.9 10.9 1.0
CB A:ASP176 3.9 10.4 1.0
CB A:ASP178 3.9 10.7 1.0
C A:LEU177 4.0 10.0 1.0
N A:LEU177 4.1 10.0 1.0
CB A:SER199 4.1 12.7 1.0
CA A:LEU177 4.2 10.1 1.0
CA A:ASP176 4.3 10.6 1.0
N A:GLY182 4.3 11.7 1.0
ND1 A:HIS201 4.3 12.4 1.0
CA A:HIS201 4.4 11.2 1.0
OD2 A:ASP176 4.4 14.8 1.0
CA A:SER199 4.4 12.5 1.0
N A:HIS201 4.4 10.8 1.0
CA A:HIS181 4.4 9.6 1.0
C A:SER199 4.5 12.3 1.0
N A:HIS180 4.5 9.2 1.0
CA A:LEU200 4.5 11.1 1.0
N A:HIS181 4.5 9.9 1.0
O A:HOH575 4.5 12.2 1.0
CG A:HIS201 4.6 10.6 1.0
C A:LEU179 4.7 9.7 1.0
C A:HIS181 4.7 10.9 1.0
N A:LEU179 4.7 9.0 1.0
O A:LEU177 4.7 11.1 1.0
CA A:HIS180 4.8 9.0 1.0
CE1 A:HIS142 4.8 11.7 1.0
O A:LEU179 5.0 10.3 1.0

Potassium binding site 2 out of 4 in 5d1c

Go back to Potassium Binding Sites List in 5d1c
Potassium binding site 2 out of 4 in the Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:14.7
occ:1.00
 O A:VAL195 2.6 18.2 1.0
O A:PHE189 2.6 15.3 1.0
O A:HOH588 2.7 15.0 1.0
O A:THR192 2.8 18.2 1.0
O A:HOH710 2.9 16.2 1.0
O A:TYR225 3.0 15.0 1.0
C A:PHE189 3.6 15.0 1.0
CB A:TYR225 3.7 15.1 1.0
C A:TYR225 3.7 15.9 1.0
C A:VAL195 3.8 16.5 1.0
C A:THR192 4.0 16.0 1.0
CB A:PHE189 4.1 14.9 1.0
OG A:SER226 4.1 19.0 1.0
CA A:TYR225 4.3 15.6 1.0
CA A:MET196 4.4 14.7 0.7
N A:SER190 4.4 14.8 1.0
CA A:PHE189 4.4 14.6 1.0
CA A:MET196 4.4 15.3 0.3
O A:SER190 4.5 17.5 1.0
CA A:SER190 4.5 15.3 1.0
CG2 A:THR192 4.5 17.7 1.0
N A:THR192 4.5 17.2 1.0
N A:SER226 4.5 14.3 1.0
C A:SER190 4.5 16.1 1.0
N A:MET196 4.6 14.1 1.0
N A:THR197 4.6 13.7 1.0
O A:GLY222 4.6 17.6 1.0
CA A:THR192 4.8 16.5 1.0
CA A:VAL195 4.8 15.2 1.0
OG1 A:THR197 4.9 17.8 1.0
CA A:GLY222 4.9 17.1 1.0
N A:VAL195 4.9 15.5 1.0
CG A:TYR225 5.0 16.2 1.0
CG2 A:THR197 5.0 16.5 1.0
C A:MET196 5.0 13.9 1.0
CB A:VAL195 5.0 14.6 1.0
CA A:SER226 5.0 15.2 1.0

Potassium binding site 3 out of 4 in 5d1c

Go back to Potassium Binding Sites List in 5d1c
Potassium binding site 3 out of 4 in the Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K401

b:9.5
occ:1.00
 OD1 B:ASP176 2.7 10.9 1.0
O B:ASP178 2.7 10.2 1.0
O B:LEU200 2.7 10.3 1.0
O B:HIS180 2.7 8.9 1.0
O B:ASP176 2.8 10.1 1.0
OG B:SER199 2.9 11.4 1.0
CG B:ASP176 3.4 11.2 1.0
C B:ASP176 3.4 9.6 1.0
N B:ASP178 3.5 9.5 1.0
C B:ASP178 3.6 8.8 1.0
C B:LEU200 3.7 11.0 1.0
C B:HIS180 3.8 8.2 1.0
CB B:HIS201 3.9 9.9 1.0
CB B:ASP176 3.9 9.6 1.0
N B:LEU200 3.9 9.7 1.0
CA B:ASP178 3.9 9.4 1.0
CB B:ASP178 4.0 9.8 1.0
C B:LEU177 4.0 8.4 1.0
N B:LEU177 4.0 9.3 1.0
CB B:SER199 4.1 11.6 1.0
CA B:LEU177 4.2 8.8 1.0
CA B:ASP176 4.3 9.3 1.0
OD2 B:ASP176 4.3 12.6 1.0
ND1 B:HIS201 4.3 10.9 1.0
N B:GLY182 4.3 10.8 1.0
CA B:SER199 4.4 9.7 1.0
CA B:HIS201 4.4 10.0 1.0
N B:HIS180 4.4 8.8 1.0
CA B:HIS181 4.4 9.5 1.0
N B:HIS201 4.5 10.3 1.0
C B:SER199 4.5 10.8 1.0
N B:HIS181 4.5 8.4 1.0
CA B:LEU200 4.5 10.9 1.0
O B:HOH582 4.6 11.2 1.0
CG B:HIS201 4.6 10.0 1.0
C B:LEU179 4.6 9.4 1.0
C B:HIS181 4.7 9.9 1.0
N B:LEU179 4.7 9.3 1.0
CA B:HIS180 4.7 9.0 1.0
O B:LEU177 4.8 10.1 1.0
CE1 B:HIS142 4.8 10.2 1.0
O B:LEU179 5.0 10.2 1.0

Potassium binding site 4 out of 4 in 5d1c

Go back to Potassium Binding Sites List in 5d1c
Potassium binding site 4 out of 4 in the Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:12.8
occ:1.00
 O B:VAL195 2.6 14.1 1.0
O B:PHE189 2.6 13.3 1.0
O B:HOH575 2.7 13.9 1.0
O B:THR192 2.8 15.6 1.0
O B:HOH719 2.9 14.4 1.0
O B:TYR225 2.9 13.7 1.0
C B:PHE189 3.6 13.8 1.0
CB B:TYR225 3.6 13.9 1.0
C B:TYR225 3.7 15.0 1.0
C B:VAL195 3.8 12.9 1.0
CB B:PHE189 4.0 14.3 1.0
C B:THR192 4.0 14.4 1.0
OG B:SER226 4.1 15.9 1.0
CA B:TYR225 4.3 13.2 1.0
CA B:PHE189 4.4 11.9 1.0
CA B:MET196 4.4 10.5 0.6
N B:SER190 4.4 12.7 1.0
O B:SER190 4.5 16.1 1.0
CA B:SER190 4.5 13.6 1.0
N B:SER226 4.5 12.3 1.0
CG2 B:THR192 4.5 22.1 1.0
C B:SER190 4.5 15.2 1.0
CA B:MET196 4.6 11.2 0.4
N B:THR192 4.6 15.5 1.0
N B:MET196 4.6 11.7 0.6
N B:MET196 4.6 11.7 0.4
N B:THR197 4.7 11.6 1.0
O B:GLY222 4.7 16.6 1.0
CA B:THR192 4.8 16.3 1.0
CA B:VAL195 4.8 12.8 1.0
OG1 B:THR197 4.9 15.1 1.0
CB B:VAL195 4.9 11.4 1.0
CG B:TYR225 4.9 14.5 1.0
N B:SER193 5.0 15.0 1.0
N B:VAL195 5.0 11.5 1.0
CA B:SER226 5.0 12.8 1.0
C B:MET196 5.0 11.0 0.4

Reference:

C.Decroos, N.H.Christianson, L.E.Gullett, C.M.Bowman, K.E.Christianson, M.A.Deardorff, D.W.Christianson. Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia De Lange Syndrome Spectrum Disorders. Biochemistry V. 54 6501 2015.
ISSN: ISSN 0006-2960
PubMed: 26463496
DOI: 10.1021/ACS.BIOCHEM.5B00881
Page generated: Mon Aug 12 13:09:23 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