Zinc in PDB 9ggm: Cryo-Em Structure of KBTBD4 P313PRR Mutant-HDAC2 2:2 Complex

All present enzymatic activity of Cryo-Em Structure of KBTBD4 P313PRR Mutant-HDAC2 2:2 Complex:
3.5.1.98;

The binding sites of Zinc atom in the Cryo-Em Structure of KBTBD4 P313PRR Mutant-HDAC2 2:2 Complex (pdb code 9ggm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of KBTBD4 P313PRR Mutant-HDAC2 2:2 Complex, PDB code: 9ggm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of KBTBD4 P313PRR Mutant-HDAC2 2:2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of KBTBD4 P313PRR Mutant-HDAC2 2:2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:187.7 occ:1.00 OD2 D:ASP265 2.1 100.4 1.0 OD1 D:ASP177 2.2 113.9 1.0 ND1 D:HIS179 2.3 113.9 1.0 OD2 D:ASP177 2.5 113.9 1.0 CG D:ASP177 2.6 113.9 1.0 CE1 D:HIS179 3.0 113.9 1.0 CG D:ASP265 3.1 100.4 1.0 OD1 D:ASP265 3.5 100.4 1.0 CG D:HIS179 3.5 113.9 1.0 CB D:HIS179 3.9 113.9 1.0 CB D:ASP177 4.1 113.9 1.0 N D:HIS179 4.1 113.9 1.0 NE2 D:HIS141 4.2 113.9 1.0 NE2 D:HIS179 4.3 113.9 1.0 CA D:GLY302 4.3 113.9 1.0 CE1 D:HIS141 4.3 113.9 1.0 N D:ILE178 4.4 113.9 1.0 N D:GLY302 4.5 113.9 1.0 CB D:ASP265 4.5 100.4 1.0 CD2 D:HIS179 4.5 113.9 1.0 CG2 D:ILE178 4.5 113.9 1.0 CA D:HIS179 4.7 113.9 1.0 CA D:ASP177 4.9 113.9 1.0 NE2 D:GLN261 5.0 113.9 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of KBTBD4 P313PRR Mutant-HDAC2 2:2 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of KBTBD4 P313PRR Mutant-HDAC2 2:2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:187.7 occ:1.00 OD2 B:ASP265 2.1 100.4 1.0 OD1 B:ASP177 2.2 113.9 1.0 ND1 B:HIS179 2.3 113.9 1.0 OD2 B:ASP177 2.5 113.9 1.0 CG B:ASP177 2.6 113.9 1.0 CE1 B:HIS179 3.0 113.9 1.0 CG B:ASP265 3.1 100.4 1.0 OD1 B:ASP265 3.5 100.4 1.0 CG B:HIS179 3.5 113.9 1.0 CB B:HIS179 3.9 113.9 1.0 CB B:ASP177 4.1 113.9 1.0 N B:HIS179 4.1 113.9 1.0 NE2 B:HIS141 4.2 113.9 1.0 NE2 B:HIS179 4.3 113.9 1.0 CA B:GLY302 4.3 113.9 1.0 CE1 B:HIS141 4.3 113.9 1.0 N B:ILE178 4.4 113.9 1.0 N B:GLY302 4.5 113.9 1.0 CB B:ASP265 4.5 100.4 1.0 CD2 B:HIS179 4.5 113.9 1.0 CG2 B:ILE178 4.5 113.9 1.0 CA B:HIS179 4.7 113.9 1.0 CA B:ASP177 4.9 113.9 1.0 NE2 B:GLN261 5.0 113.9 1.0

Z.Chen, G.Chi, T.Balo, X.Chen, B.R.Montes, S.C.Clifford, V.D'angiolella, T.Szabo, A.Kiss, T.Novak, A.Herner, A.Kotschy, A.N.Bullock. Structural Mimicry of UM171 and Neomorphic Cancer Mutants Co-Opts E3 Ligase KBTBD4 For HDAC1/2 Recruitment. Nat Commun V. 16 3144 2025.
ISSN: ESSN 2041-1723
PubMed: 40175372
DOI: 10.1038/S41467-025-58350-Z