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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 Aug 12 16:11:01 2024

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