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Potassium in PDB 5vi6: Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A

Enzymatic activity of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A

All present enzymatic activity of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A, PDB code: 5vi6 was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.29 / 1.24
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 50.980, 50.980, 116.517, 90.00, 90.00, 120.00
R / Rfree (%) 12.1 / 14.3

Other elements in 5vi6:

The structure of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A (pdb code 5vi6). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A, PDB code: 5vi6:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 5vi6

Go back to Potassium Binding Sites List in 5vi6
Potassium binding site 1 out of 2 in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A


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 Histone Deacetylase 8 in Complex with Trapoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:8.5
occ:1.00
O A:LEU200 2.7 9.2 1.0
OD1 A:ASP176 2.7 9.0 1.0
O A:ASP178 2.7 8.9 1.0
O A:HIS180 2.8 8.8 1.0
O A:ASP176 2.8 8.9 1.0
HG A:SER199 2.8 10.8 1.0
HB3 A:HIS201 2.9 10.1 1.0
OG A:SER199 2.9 9.0 1.0
HB3 A:ASP178 3.3 10.3 1.0
H A:ASP178 3.4 10.3 1.0
C A:ASP176 3.4 8.7 1.0
CG A:ASP176 3.4 8.4 1.0
HB3 A:ASP176 3.5 11.1 1.0
H A:LEU200 3.5 10.8 1.0
N A:ASP178 3.5 8.6 1.0
C A:ASP178 3.6 8.1 1.0
C A:LEU200 3.6 8.9 1.0
C A:HIS180 3.7 8.3 1.0
HA A:HIS181 3.7 10.9 1.0
CB A:HIS201 3.8 8.4 1.0
H A:GLY182 3.8 10.7 1.0
HA A:LEU177 3.9 9.8 1.0
CB A:ASP176 3.9 9.2 1.0
HA A:SER199 3.9 10.6 1.0
N A:LEU200 3.9 9.0 1.0
CA A:ASP178 3.9 8.2 1.0
C A:LEU177 4.0 8.9 1.0
CB A:ASP178 4.0 8.6 1.0
N A:LEU177 4.0 8.3 1.0
HE1 A:HIS142 4.0 10.8 1.0
CB A:SER199 4.1 9.5 1.0
HA A:HIS201 4.1 11.4 1.0
CA A:LEU177 4.2 8.2 1.0
N A:GLY182 4.3 8.9 1.0
CA A:ASP176 4.3 8.8 1.0
ND1 A:HIS201 4.3 9.9 1.0
CA A:HIS201 4.3 9.5 1.0
CA A:SER199 4.3 8.8 1.0
OD2 A:ASP176 4.3 9.4 1.0
HB2 A:ASP178 4.4 10.3 1.0
HB2 A:HIS201 4.4 10.1 1.0
CA A:HIS181 4.4 9.1 1.0
HB2 A:SER199 4.4 11.4 1.0
N A:HIS181 4.4 8.5 1.0
N A:HIS180 4.4 8.3 1.0
N A:HIS201 4.4 9.2 1.0
H A:HIS180 4.4 9.9 1.0
C A:SER199 4.5 8.7 1.0
CA A:LEU200 4.5 9.1 1.0
CG A:HIS201 4.5 8.9 1.0
O A:HOH621 4.6 10.8 1.0
C A:HIS181 4.6 9.3 1.0
C A:LEU179 4.6 8.6 1.0
H A:LEU177 4.7 10.0 1.0
HD1 A:HIS142 4.7 10.3 1.0
CA A:HIS180 4.7 8.7 1.0
N A:LEU179 4.7 9.0 1.0
O A:LEU177 4.7 9.4 1.0
HB3 A:SER199 4.8 11.4 1.0
HB2 A:ASP176 4.8 11.1 1.0
HA A:ASP176 4.8 10.6 1.0
CE1 A:HIS142 4.8 9.0 1.0
HB2 A:LEU200 4.8 11.8 1.0
HA A:ASP178 4.9 9.9 1.0
HA3 A:GLY182 4.9 10.9 1.0
O A:LEU179 4.9 9.5 1.0

Potassium binding site 2 out of 2 in 5vi6

Go back to Potassium Binding Sites List in 5vi6
Potassium binding site 2 out of 2 in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A


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 Histone Deacetylase 8 in Complex with Trapoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:12.0
occ:1.00
O A:VAL195 2.6 14.2 1.0
O A:PHE189 2.6 12.5 1.0
O A:HOH590 2.7 13.0 1.0
O A:HOH730 2.8 12.2 1.0
O A:THR192 2.8 15.8 1.0
O A:TYR225 3.0 12.8 1.0
HB3 A:TYR225 3.0 16.8 1.0
HB2 A:TYR225 3.2 16.8 1.0
HB3 A:PHE189 3.4 15.0 1.0
CB A:TYR225 3.5 14.0 1.0
HA A:MET196 3.6 14.3 0.7
C A:PHE189 3.6 11.7 1.0
C A:TYR225 3.6 12.5 1.0
HA A:MET196 3.7 14.4 0.3
HA A:SER190 3.7 17.1 0.3
HG23 A:THR192 3.8 20.3 1.0
C A:VAL195 3.8 13.2 1.0
H A:THR192 3.8 17.1 1.0
HA A:SER190 3.9 15.5 0.7
HB2 A:PHE189 3.9 15.0 1.0
CB A:PHE189 4.0 12.5 1.0
C A:THR192 4.0 14.8 1.0
H A:THR197 4.0 13.0 0.7
H A:THR197 4.1 13.0 0.3
HG1 A:THR197 4.1 14.0 1.0
HG23 A:THR197 4.1 14.9 1.0
OG A:SER226 4.2 13.7 1.0
HG22 A:THR192 4.2 20.3 1.0
CA A:TYR225 4.2 12.8 1.0
O A:SER190 4.3 13.6 0.7
CA A:SER190 4.3 14.2 0.3
HB A:VAL195 4.3 15.3 1.0
H A:VAL195 4.4 15.9 1.0
HA3 A:GLY222 4.4 18.8 1.0
C A:SER190 4.4 13.8 0.7
CA A:SER190 4.4 12.9 0.7
N A:SER190 4.4 13.2 0.3
CA A:MET196 4.4 11.9 0.7
N A:SER190 4.4 13.0 0.7
CA A:PHE189 4.4 11.8 1.0
CG2 A:THR192 4.4 16.9 1.0
N A:SER226 4.5 11.8 1.0
CA A:MET196 4.5 12.0 0.3
N A:THR192 4.5 14.3 1.0
C A:SER190 4.5 14.1 0.3
HA2 A:GLY222 4.5 18.8 1.0
O A:SER190 4.6 13.8 0.3
N A:MET196 4.6 11.9 0.7
N A:MET196 4.6 12.4 0.3
HA A:SER193 4.6 20.7 1.0
O A:GLY222 4.6 14.3 1.0
HG A:SER226 4.7 16.4 1.0
N A:THR197 4.7 10.8 1.0
HG12 A:VAL195 4.7 16.2 1.0
CA A:THR192 4.8 14.4 1.0
HA A:SER226 4.8 14.3 1.0
CG A:TYR225 4.8 14.4 1.0
CA A:VAL195 4.8 13.1 1.0
HA A:TYR225 4.9 15.3 1.0
CA A:GLY222 4.9 15.6 1.0
HA A:PHE189 4.9 14.2 1.0
OG1 A:THR197 4.9 11.7 1.0
C A:MET196 5.0 10.6 0.3
H A:SER226 5.0 14.2 1.0
N A:VAL195 5.0 13.2 1.0
H A:TYR225 5.0 15.5 1.0

Reference:

N.J.Porter, D.W.Christianson. Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8. Acs Chem. Biol. V. 12 2281 2017.
ISSN: ESSN 1554-8937
PubMed: 28846375
DOI: 10.1021/ACSCHEMBIO.7B00330
Page generated: Mon Dec 14 00:10:11 2020

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