Zinc in PDB 7klo: Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A

All present enzymatic activity of Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A:
1.14.11.67;

The binding sites of Zinc atom in the Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A (pdb code 7klo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A, PDB code: 7klo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:0.0 occ:1.00 ND1 A:HIS319 2.0 0.0 1.0 SG A:CYS322 2.3 0.0 1.0 SG A:CYS299 2.3 0.0 1.0 SG A:CYS296 2.3 0.0 1.0 CE1 A:HIS319 2.9 0.0 1.0 HB2 A:HIS319 2.9 0.0 1.0 H A:HIS319 2.9 0.0 1.0 CG A:HIS319 3.0 0.0 1.0 HE1 A:HIS319 3.1 0.0 1.0 HB2 A:MET297 3.2 0.0 1.0 HB3 A:CYS296 3.2 0.0 1.0 CB A:CYS322 3.4 0.0 1.0 HB2 A:CYS322 3.4 0.0 1.0 CB A:CYS296 3.4 0.0 1.0 CB A:CYS299 3.4 0.0 1.0 CB A:HIS319 3.5 0.0 1.0 HB2 A:CYS299 3.6 0.0 1.0 HB3 A:CYS299 3.6 0.0 1.0 HD13 A:LEU308 3.6 0.0 1.0 HB3 A:CYS322 3.6 0.0 1.0 N A:HIS319 3.8 0.0 1.0 NE2 A:HIS319 4.0 0.0 1.0 CD2 A:HIS319 4.1 0.0 1.0 HB2 A:CYS296 4.1 0.0 1.0 H A:MET297 4.1 0.0 1.0 HA A:TYR318 4.2 0.0 1.0 CB A:MET297 4.2 0.0 1.0 N A:MET297 4.2 0.0 1.0 CA A:HIS319 4.3 0.0 1.0 HB3 A:HIS319 4.4 0.0 1.0 CD1 A:LEU308 4.5 0.0 1.0 C A:CYS296 4.6 0.0 1.0 CA A:CYS296 4.6 0.0 1.0 O A:MET297 4.6 0.0 1.0 HD12 A:LEU308 4.6 0.0 1.0 CA A:MET297 4.6 0.0 1.0 HD2 A:TYR318 4.7 0.0 1.0 HG2 A:MET297 4.7 0.0 1.0 HE2 A:HIS319 4.7 0.0 1.0 HB3 A:MET297 4.8 0.0 1.0 CA A:CYS322 4.8 0.0 1.0 CA A:CYS299 4.8 0.0 1.0 HD11 A:LEU308 4.8 0.0 1.0 H A:CYS299 4.9 0.0 1.0 C A:TYR318 4.9 0.0 1.0 C A:MET297 4.9 0.0 1.0 HA A:HIS319 4.9 0.0 1.0 CG A:MET297 5.0 0.0 1.0 HA A:CYS322 5.0 0.0 1.0 CA A:TYR318 5.0 0.0 1.0

Zinc binding site 2 out of 2 in the Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:0.0 occ:1.00 SG A:CYS311 2.3 0.0 1.0 SG A:CYS340 2.3 0.0 1.0 SG A:CYS337 2.3 0.0 1.0 SG A:CYS314 2.3 0.0 1.0 H A:CYS337 2.9 0.0 1.0 HB2 A:CYS340 3.2 0.0 1.0 HB2 A:CYS314 3.3 0.0 1.0 HB3 A:CYS311 3.3 0.0 1.0 HB3 A:CYS337 3.4 0.0 1.0 CB A:CYS311 3.4 0.0 1.0 CB A:CYS340 3.4 0.0 1.0 CB A:CYS314 3.4 0.0 1.0 CB A:CYS337 3.4 0.0 1.0 H A:CYS340 3.6 0.0 1.0 HB2 A:CYS311 3.7 0.0 1.0 N A:CYS337 3.8 0.0 1.0 HB3 A:CYS314 3.8 0.0 1.0 HB2 A:ASP316 3.8 0.0 1.0 HB3 A:CYS340 4.1 0.0 1.0 CA A:CYS337 4.1 0.0 1.0 H A:ASP312 4.3 0.0 1.0 HB2 A:LYS339 4.3 0.0 1.0 HB2 A:CYS337 4.3 0.0 1.0 N A:CYS340 4.3 0.0 1.0 HA A:ARG336 4.4 0.0 1.0 CA A:CYS340 4.4 0.0 1.0 H A:CYS314 4.5 0.0 1.0 O A:CYS337 4.6 0.0 1.0 H A:GLY313 4.7 0.0 1.0 HB2 A:ASP312 4.7 0.0 1.0 CA A:CYS314 4.7 0.0 1.0 HA A:CYS340 4.8 0.0 1.0 CB A:ASP316 4.8 0.0 1.0 OD1 A:ASP312 4.8 0.0 1.0 C A:CYS337 4.8 0.0 1.0 CA A:CYS311 4.8 0.0 1.0 N A:ASP312 4.9 0.0 1.0 C A:ARG336 4.9 0.0 1.0 N A:CYS314 4.9 0.0 1.0 HB3 A:ASP316 4.9 0.0 1.0 HB3 A:ARG336 4.9 0.0 1.0

J.E.Longbotham, M.J.S.Kelly, D.G.Fujimori. Recognition of Histone H3 Methylation States By the PHD1 Domain of Histone Demethylase KDM5A. Acs Chem.Biol. 2021.
ISSN: ESSN 1554-8937
PubMed: 33621062
DOI: 10.1021/ACSCHEMBIO.0C00976