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

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

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

Potassium

(K)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the A Degradation Product of Pd 404182 (P2742) Bound to Histone Deacetylase-Like Amidohydrolase, PDB code: 6gjk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn401 b:10.5 occ:0.70 OD2 A:ASP268 2.0 9.8 1.0 OD1 A:ASP180 2.0 9.3 1.0 ND1 A:HIS182 2.1 10.1 1.0 O A:ACT409 2.1 14.1 1.0 OXT A:ACT409 2.1 15.0 1.0 C A:ACT409 2.4 15.8 1.0 OD2 A:ASP180 2.5 10.8 1.0 CG A:ASP180 2.6 8.9 1.0 CG A:ASP268 3.0 10.0 1.0 CE1 A:HIS182 3.0 11.5 1.0 CG A:HIS182 3.1 10.0 1.0 OD1 A:ASP268 3.4 9.4 1.0 CB A:HIS182 3.6 12.4 1.0 N A:HIS182 3.9 11.5 1.0 CH3 A:ACT409 4.0 16.9 1.0 NE2 A:HIS142 4.1 13.3 1.0 CB A:ASP180 4.1 9.7 1.0 NE2 A:HIS182 4.1 11.1 1.0 CD2 A:HIS182 4.2 10.2 1.0 CG1 A:VAL181 4.2 9.0 1.0 CB A:ASP268 4.2 9.2 1.0 CA A:GLY310 4.3 10.4 1.0 N A:VAL181 4.3 9.4 1.0 CA A:HIS182 4.3 12.7 1.0 CE2 A:TYR312 4.4 11.1 1.0 CE1 A:HIS142 4.5 13.2 1.0 N A:GLY310 4.6 10.1 1.0 OH A:TYR312 4.6 12.3 1.0 NE2 A:HIS143 4.7 13.4 1.0 C A:ASP180 4.8 10.2 1.0 CA A:ASP180 4.8 10.3 1.0 C A:VAL181 4.9 9.5 1.0 C A:GLY310 4.9 11.2 1.0 N A:GLY311 4.9 11.6 1.0 CZ A:TYR312 5.0 11.8 1.0

Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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 B:Zn401 b:9.8 occ:0.70 OD2 B:ASP268 2.0 9.3 1.0 OD1 B:ASP180 2.0 9.0 1.0 OXT B:ACT411 2.1 13.3 1.0 ND1 B:HIS182 2.1 9.1 1.0 O B:ACT411 2.1 14.1 1.0 C B:ACT411 2.4 14.5 1.0 OD2 B:ASP180 2.5 9.8 1.0 CG B:ASP180 2.6 8.2 1.0 CG B:ASP268 2.9 9.4 1.0 CE1 B:HIS182 3.0 10.3 1.0 CG B:HIS182 3.1 8.7 1.0 OD1 B:ASP268 3.3 8.4 1.0 CB B:HIS182 3.6 7.4 1.0 N B:HIS182 3.9 8.1 1.0 CH3 B:ACT411 3.9 15.6 1.0 NE2 B:HIS142 4.1 11.9 1.0 CB B:ASP180 4.1 8.6 1.0 NE2 B:HIS182 4.1 9.8 1.0 CD2 B:HIS182 4.2 9.7 1.0 CB B:ASP268 4.2 8.7 1.0 CA B:GLY310 4.2 9.6 1.0 CG1 B:VAL181 4.3 9.0 1.0 N B:VAL181 4.3 8.5 1.0 CA B:HIS182 4.4 7.3 1.0 CE2 B:TYR312 4.4 9.5 1.0 CE1 B:HIS142 4.4 10.2 1.0 N B:GLY310 4.5 9.2 1.0 OH B:TYR312 4.6 11.5 1.0 C B:ASP180 4.7 8.7 1.0 CA B:ASP180 4.8 8.6 1.0 NE2 B:HIS143 4.8 12.6 1.0 C B:VAL181 4.8 8.1 1.0 C B:GLY310 4.9 9.9 1.0 N B:GLY311 4.9 10.3 1.0 CA B:VAL181 5.0 8.6 1.0 CZ B:TYR312 5.0 10.3 1.0

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