Atomistry » Potassium » PDB 6f3o-6h6x » 6gjk
Atomistry »
  Potassium »
    PDB 6f3o-6h6x »
      6gjk »

Potassium in PDB 6gjk: A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase

Protein crystallography data

The structure of A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase, PDB code: 6gjk was solved by A.Kraemer, F.J.Meyer-Almes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.77 / 1.47
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.680, 100.680, 175.530, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.4

Other elements in 6gjk:

The structure of A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase (pdb code 6gjk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase, PDB code: 6gjk:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6gjk

Go back to Potassium Binding Sites List in 6gjk
Potassium binding site 1 out of 4 in the A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:16.9
occ:0.90
 O A:ASP180 2.6 9.9 1.0
OG A:SER201 2.8 10.8 1.0
O A:HIS182 2.8 10.7 1.0
OD1 A:ASP178 3.0 14.1 1.0
O A:LEU202 3.1 14.6 1.0
CG A:ASP178 3.2 11.5 1.0
O A:ASP178 3.2 12.8 1.0
OD2 A:ASP178 3.4 12.6 1.0
C A:ASP180 3.7 10.2 1.0
C A:ASP178 3.7 9.6 1.0
C A:HIS182 3.8 9.4 1.0
CB A:SER201 3.8 9.7 1.0
C A:LEU202 3.9 12.1 1.0
CB A:ASP178 3.9 11.7 1.0
N A:LEU202 3.9 10.2 1.0
CB A:HIS203 3.9 11.6 1.0
N A:ASP180 3.9 10.2 1.0
N A:GLY184 4.0 9.6 1.0
CA A:SER201 4.0 9.3 1.0
C A:SER201 4.2 9.6 1.0
CA A:ASP180 4.2 10.3 1.0
CA A:HIS183 4.3 9.5 1.0
C A:TRP179 4.3 9.4 1.0
N A:TRP179 4.3 8.8 1.0
CB A:ASP180 4.4 9.7 1.0
CA A:ASP178 4.4 10.1 1.0
CA A:TRP179 4.4 10.7 1.0
C A:HIS183 4.4 10.2 1.0
ND1 A:HIS142 4.4 11.9 1.0
CE1 A:HIS142 4.5 13.2 1.0
N A:HIS183 4.5 9.0 1.0
CA A:HIS203 4.5 10.9 1.0
N A:HIS203 4.5 11.2 1.0
N A:HIS182 4.6 11.5 1.0
CD2 A:HIS203 4.6 12.7 1.0
CG A:HIS203 4.6 12.2 1.0
CA A:LEU202 4.6 11.8 1.0
N A:VAL181 4.8 9.4 1.0
CA A:GLY184 4.8 10.4 1.0
C A:VAL181 4.8 9.5 1.0
CA A:HIS182 4.9 12.7 1.0
O A:HOH568 4.9 13.9 1.0

Potassium binding site 2 out of 4 in 6gjk

Go back to Potassium Binding Sites List in 6gjk
Potassium binding site 2 out of 4 in the A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:12.2
occ:1.00
 O A:VAL197 2.7 12.5 1.0
O A:HOH607 2.7 12.2 1.0
O A:TRP191 2.7 11.9 1.0
O A:HOH617 2.9 11.2 1.0
O A:ASP194 2.9 14.5 1.0
O A:TYR226 2.9 11.8 1.0
C A:TRP191 3.6 10.9 1.0
CB A:TRP191 3.6 11.3 1.0
OG1 A:THR199 3.7 12.1 1.0
C A:TYR226 3.7 11.0 1.0
C A:VAL197 3.9 10.8 1.0
C A:ASP194 4.0 12.7 1.0
CB A:TYR226 4.1 11.5 1.0
CA A:TRP191 4.2 11.3 1.0
CG2 A:THR199 4.3 11.2 1.0
N A:THR199 4.3 10.1 1.0
N A:ASN227 4.5 10.2 1.0
CA A:TYR226 4.5 10.7 1.0
N A:TRP192 4.5 11.0 1.0
CB A:THR199 4.5 11.2 1.0
N A:ASP194 4.6 12.7 1.0
CA A:LEU198 4.6 10.7 1.0
N A:LEU198 4.7 10.4 1.0
CA A:ASP194 4.7 13.9 1.0
O A:TRP192 4.7 12.1 1.0
CB A:ASN227 4.8 11.0 1.0
CA A:TRP192 4.8 11.3 1.0
CA A:ASN227 4.8 10.4 1.0
C A:TRP192 4.8 12.1 1.0
C A:LEU198 4.8 10.6 1.0
CA A:VAL197 4.9 10.6 1.0
CG A:TRP191 4.9 11.4 1.0
O A:GLY223 4.9 13.5 1.0
CB A:ASP194 5.0 13.7 1.0
N A:VAL197 5.0 11.0 1.0
N A:PRO195 5.0 13.1 1.0

Potassium binding site 3 out of 4 in 6gjk

Go back to Potassium Binding Sites List in 6gjk
Potassium binding site 3 out of 4 in the A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:14.2
occ:0.80
 O B:ASP180 2.6 8.8 1.0
OG B:SER201 2.7 10.3 1.0
O B:HIS182 2.8 9.6 1.0
O B:LEU202 3.0 15.5 1.0
OD1 B:ASP178 3.0 12.8 1.0
CG B:ASP178 3.2 11.4 1.0
O B:ASP178 3.2 11.9 1.0
OD2 B:ASP178 3.4 12.0 1.0
C B:ASP180 3.6 8.7 1.0
C B:ASP178 3.7 9.5 1.0
C B:HIS182 3.8 8.1 1.0
CB B:SER201 3.8 9.3 1.0
C B:LEU202 3.8 11.7 1.0
CB B:ASP178 3.9 11.0 1.0
CB B:HIS203 3.9 10.9 1.0
N B:ASP180 3.9 8.4 1.0
N B:LEU202 3.9 8.9 1.0
N B:GLY184 4.0 9.5 1.0
CA B:SER201 4.0 8.5 1.0
CA B:ASP180 4.2 8.6 1.0
C B:SER201 4.2 8.9 1.0
CA B:HIS183 4.3 8.4 1.0
N B:TRP179 4.3 9.3 1.0
C B:TRP179 4.3 8.8 1.0
CB B:ASP180 4.3 8.6 1.0
CA B:TRP179 4.4 9.3 1.0
CA B:ASP178 4.4 9.5 1.0
C B:HIS183 4.4 8.9 1.0
ND1 B:HIS142 4.4 10.4 1.0
CE1 B:HIS142 4.5 10.2 1.0
N B:HIS183 4.5 8.2 1.0
ND1 B:HIS203 4.5 13.5 1.0
CA B:HIS203 4.5 10.1 1.0
N B:HIS203 4.5 10.8 1.0
N B:HIS182 4.5 8.1 1.0
CA B:LEU202 4.6 11.3 1.0
CG B:HIS203 4.6 11.3 1.0
N B:VAL181 4.7 8.5 1.0
CA B:GLY184 4.8 10.2 1.0
C B:VAL181 4.8 8.1 1.0
CA B:HIS182 4.9 7.3 1.0
O B:HOH614 4.9 11.0 1.0

Potassium binding site 4 out of 4 in 6gjk

Go back to Potassium Binding Sites List in 6gjk
Potassium binding site 4 out of 4 in the A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:12.5
occ:1.00
 O B:VAL197 2.7 11.1 1.0
O B:HOH646 2.7 12.1 1.0
O B:TRP191 2.7 11.8 1.0
O B:TYR226 2.9 11.9 1.0
O B:ASP194 2.9 14.9 1.0
O B:HOH626 3.0 12.1 1.0
C B:TRP191 3.6 11.7 1.0
CB B:TRP191 3.6 11.5 1.0
OG1 B:THR199 3.6 11.6 1.0
C B:TYR226 3.7 11.4 1.0
C B:VAL197 3.9 11.3 1.0
C B:ASP194 4.0 14.4 1.0
CB B:TYR226 4.0 12.2 1.0
CA B:TRP191 4.2 11.2 1.0
N B:THR199 4.3 10.3 1.0
CG2 B:THR199 4.3 11.2 1.0
N B:ASN227 4.4 11.2 1.0
CA B:TYR226 4.5 11.1 1.0
N B:TRP192 4.5 11.3 1.0
CB B:THR199 4.5 10.9 1.0
CA B:LEU198 4.6 11.3 1.0
N B:ASP194 4.6 15.5 1.0
N B:LEU198 4.7 11.0 1.0
CA B:ASP194 4.7 16.0 1.0
O B:TRP192 4.8 13.0 1.0
CA B:ASN227 4.8 10.3 1.0
CA B:TRP192 4.8 11.7 1.0
CB B:ASN227 4.8 11.1 1.0
C B:LEU198 4.8 11.0 1.0
C B:TRP192 4.8 12.7 1.0
CG B:TRP191 4.9 11.3 1.0
CA B:VAL197 4.9 11.3 1.0
N B:PRO195 4.9 14.0 1.0
CA B:PRO195 5.0 14.2 1.0
O B:GLY223 5.0 13.1 1.0
CB B:ASP194 5.0 16.3 1.0

Reference:

M.Muth, N.Jansch, A.Kopranovic, A.Kramer, N.Wossner, M.Jung, F.Kirschhofer, F.J.Meyer-Almes. Covalent Inhibition of Histone Deacetylase 8 By 3,4-Dihydro-2H-Pyrimido[1,2-C][1,3]Benzothiazin-6-Imine. Biochim Biophys Acta Gen V.1863 577 2019SUBJ.
ISSN: ISSN 1872-8006
PubMed: 30611847
DOI: 10.1016/J.BBAGEN.2019.01.001
Page generated: Mon Dec 14 00:38:16 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy