Zinc in PDB 7ltg: Structure of Human HDAC2 in Complex with Apicidin

All present enzymatic activity of Structure of Human HDAC2 in Complex with Apicidin:
3.5.1.98;

The structure of Structure of Human HDAC2 in Complex with Apicidin, PDB code: 7ltg was solved by D.J.Klein, D.C.Beshore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.25 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.27, 98.39, 139.07, 90, 90, 90
R / Rfree (%)	16.8 / 19.8

The structure of Structure of Human HDAC2 in Complex with Apicidin also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Structure of Human HDAC2 in Complex with Apicidin (pdb code 7ltg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Human HDAC2 in Complex with Apicidin, PDB code: 7ltg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with Apicidin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human HDAC2 in Complex with Apicidin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:17.9 occ:1.00 OD2 A:ASP265 1.9 17.0 1.0 O2 A:YED407 1.9 23.6 1.0 OD1 A:ASP177 1.9 15.4 1.0 ND1 A:HIS179 2.1 18.9 1.0 O1 A:YED407 2.4 17.7 1.0 CG A:ASP177 2.8 15.3 1.0 C25 A:YED407 2.8 22.9 1.0 CG A:ASP265 2.9 17.5 1.0 OD2 A:ASP177 2.9 19.3 1.0 CE1 A:HIS179 3.0 18.0 1.0 CG A:HIS179 3.2 18.1 1.0 OD1 A:ASP265 3.3 15.2 1.0 CB A:HIS179 3.6 16.1 1.0 C26 A:YED407 3.8 26.0 1.0 N A:HIS179 3.9 15.9 1.0 C24 A:YED407 3.9 18.7 1.0 CA A:GLY302 4.0 16.4 1.0 C23 A:YED407 4.0 19.4 1.0 CG2 A:ILE178 4.1 16.3 1.0 NE2 A:HIS179 4.2 18.3 1.0 CB A:ASP177 4.2 15.8 1.0 CB A:ASP265 4.2 15.1 1.0 CD2 A:HIS179 4.3 18.8 1.0 OH A:TYR304 4.3 15.0 1.0 N A:ILE178 4.3 15.5 1.0 CA A:HIS179 4.4 15.6 1.0 N A:GLY302 4.4 16.9 1.0 CE2 A:TYR304 4.4 16.9 1.0 NE2 A:HIS141 4.4 18.4 1.0 CE1 A:HIS141 4.8 17.6 1.0 CZ A:TYR304 4.8 16.6 1.0 C A:ILE178 4.8 19.0 1.0 C A:ASP177 4.9 17.9 1.0 CA A:ASP177 4.9 14.3 1.0 C27 A:YED407 4.9 27.9 1.0 NE2 A:HIS142 5.0 20.9 1.0 CA A:ILE178 5.0 14.1 1.0

Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with Apicidin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human HDAC2 in Complex with Apicidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:16.9 occ:1.00 OD1 B:ASP177 1.9 15.6 1.0 OD2 B:ASP265 1.9 19.4 1.0 O2 B:YED409 2.0 19.9 1.0 ND1 B:HIS179 2.0 14.9 1.0 O1 B:YED409 2.5 16.4 1.0 CG B:ASP177 2.8 14.8 1.0 C25 B:YED409 2.8 20.2 1.0 CG B:ASP265 2.9 15.9 1.0 OD2 B:ASP177 2.9 15.1 1.0 CE1 B:HIS179 3.0 14.6 1.0 CG B:HIS179 3.1 14.9 1.0 OD1 B:ASP265 3.2 14.6 1.0 CB B:HIS179 3.5 12.9 1.0 C26 B:YED409 3.8 23.6 1.0 N B:HIS179 3.8 12.9 1.0 C24 B:YED409 4.0 18.6 1.0 C23 B:YED409 4.0 21.8 1.0 CA B:GLY302 4.1 17.3 1.0 NE2 B:HIS179 4.2 15.3 1.0 CG2 B:ILE178 4.2 15.7 1.0 CB B:ASP177 4.2 14.3 1.0 CD2 B:HIS179 4.2 16.1 1.0 CB B:ASP265 4.3 13.3 1.0 CA B:HIS179 4.3 12.6 1.0 NE2 B:HIS141 4.4 17.1 1.0 OH B:TYR304 4.4 16.2 1.0 CE2 B:TYR304 4.4 14.3 1.0 N B:ILE178 4.4 12.1 1.0 N B:GLY302 4.4 16.9 1.0 CE1 B:HIS141 4.8 16.6 1.0 C B:ILE178 4.9 15.9 1.0 CZ B:TYR304 4.9 15.8 1.0 C B:ASP177 4.9 17.0 1.0 CA B:ASP177 4.9 13.7 1.0 C27 B:YED409 4.9 22.1 1.0

Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with Apicidin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human HDAC2 in Complex with Apicidin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:24.1 occ:1.00 OD2 C:ASP265 1.9 24.7 1.0 OD1 C:ASP177 1.9 24.3 1.0 ND1 C:HIS179 2.0 23.9 1.0 O2 C:YED406 2.1 22.5 1.0 O1 C:YED406 2.4 21.5 1.0 CG C:ASP177 2.8 26.3 1.0 C25 C:YED406 2.8 28.2 1.0 CG C:ASP265 2.9 25.2 1.0 CE1 C:HIS179 2.9 23.3 1.0 OD2 C:ASP177 3.0 28.7 1.0 CG C:HIS179 3.1 23.0 1.0 OD1 C:ASP265 3.2 24.0 1.0 CB C:HIS179 3.5 20.3 1.0 N C:HIS179 3.8 21.3 1.0 C23 C:YED406 3.9 30.8 1.0 C24 C:YED406 3.9 28.1 1.0 C26 C:YED406 4.0 30.5 1.0 CA C:GLY302 4.0 25.3 1.0 NE2 C:HIS179 4.1 23.7 1.0 CG2 C:ILE178 4.1 23.5 1.0 CB C:ASP177 4.2 24.1 1.0 CD2 C:HIS179 4.2 24.3 1.0 CB C:ASP265 4.2 22.5 1.0 N C:ILE178 4.3 20.3 1.0 CA C:HIS179 4.3 19.9 1.0 NE2 C:HIS141 4.4 25.5 1.0 OH C:TYR304 4.4 27.1 1.0 N C:GLY302 4.4 24.7 1.0 CE2 C:TYR304 4.5 29.1 1.0 CE1 C:HIS141 4.7 24.9 1.0 C C:ILE178 4.8 24.2 1.0 C C:ASP177 4.9 24.9 1.0 NE2 C:HIS142 4.9 26.2 1.0 CA C:ASP177 4.9 22.8 1.0 CA C:ILE178 4.9 20.3 1.0 CZ C:TYR304 4.9 34.0 1.0 C27 C:YED406 5.0 30.9 1.0

D.C.Beshore, G.C.Adam, R.J.O.Barnard, C.Burlein, S.N.Gallicchio, M.K.Holloway, D.Krosky, W.Lemaire, R.W.Myers, S.Patel, M.A.Plotkin, D.A.Powell, V.Rada, C.D.Cox, P.J.Coleman, D.J.Klein, S.E.Wolkenberg. Redefining the Histone Deacetylase Inhibitor Pharmacophore: High Potency with No Zinc Cofactor Interaction. Acs Med.Chem.Lett. V. 12 540 2021.
ISSN: ISSN 1948-5875
PubMed: 33854701
DOI: 10.1021/ACSMEDCHEMLETT.1C00074