Zinc in PDB 7klr: Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide

All present enzymatic activity of Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide:
1.14.11.67;

The binding sites of Zinc atom in the Solution Structure of the PHD1 Domain of Histone Demethylase KDM5A in Complex with A Histone H3(1-10) Peptide (pdb code 7klr). 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 in Complex with A Histone H3(1-10) Peptide, PDB code: 7klr:
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 in Complex with A Histone H3(1-10) Peptide


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 in Complex with A Histone H3(1-10) Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.0 occ:1.00 ND1 A:HIS34 2.0 0.0 1.0 SG A:CYS37 2.3 0.0 1.0 SG A:CYS14 2.3 0.0 1.0 SG A:CYS11 2.3 0.0 1.0 HB2 A:HIS34 2.7 0.0 1.0 CE1 A:HIS34 2.9 0.0 1.0 CG A:HIS34 3.0 0.0 1.0 HB3 A:CYS14 3.1 0.0 1.0 HE1 A:HIS34 3.2 0.0 1.0 CB A:CYS11 3.3 0.0 1.0 HB3 A:CYS11 3.3 0.0 1.0 CB A:CYS14 3.3 0.0 1.0 CB A:HIS34 3.4 0.0 1.0 HB2 A:CYS11 3.4 0.0 1.0 HB2 A:CYS37 3.4 0.0 1.0 CB A:CYS37 3.4 0.0 1.0 HB3 A:CYS37 3.7 0.0 1.0 H A:HIS34 3.8 0.0 1.0 HB3 A:HIS34 4.0 0.0 1.0 HB2 A:CYS14 4.0 0.0 1.0 NE2 A:HIS34 4.1 0.0 1.0 CD2 A:HIS34 4.1 0.0 1.0 C A:CYS14 4.3 0.0 1.0 N A:GLY15 4.4 0.0 1.0 CA A:CYS14 4.4 0.0 1.0 H A:GLY15 4.4 0.0 1.0 CA A:HIS34 4.5 0.0 1.0 N A:HIS34 4.5 0.0 1.0 HA2 A:GLY15 4.5 0.0 1.0 HE1 A:PHE36 4.6 0.0 1.0 HZ A:PHE36 4.7 0.0 1.0 CA A:CYS11 4.8 0.0 1.0 O A:CYS14 4.8 0.0 1.0 CA A:CYS37 4.8 0.0 1.0 CE1 A:PHE36 4.8 0.0 1.0 CZ A:PHE36 4.9 0.0 1.0 CA A:GLY15 4.9 0.0 1.0 HA3 A:GLY15 4.9 0.0 1.0 H A:CYS37 4.9 0.0 1.0 HE2 A:HIS34 4.9 0.0 1.0 HB2 A:ASN19 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 in Complex with A Histone H3(1-10) Peptide


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 in Complex with A Histone H3(1-10) Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:0.0 occ:1.00 SG A:CYS52 2.3 0.0 1.0 SG A:CYS55 2.3 0.0 1.0 SG A:CYS26 2.3 0.0 1.0 SG A:CYS29 2.3 0.0 1.0 HB2 A:CYS55 2.9 0.0 1.0 HB3 A:CYS26 3.1 0.0 1.0 H A:CYS52 3.1 0.0 1.0 HB3 A:CYS52 3.1 0.0 1.0 CB A:CYS55 3.2 0.0 1.0 HB3 A:CYS29 3.3 0.0 1.0 CB A:CYS26 3.3 0.0 1.0 CB A:CYS52 3.3 0.0 1.0 CB A:CYS29 3.5 0.0 1.0 H A:CYS55 3.6 0.0 1.0 H A:CYS29 3.8 0.0 1.0 HB2 A:CYS26 3.8 0.0 1.0 N A:CYS52 3.9 0.0 1.0 HB3 A:CYS55 4.0 0.0 1.0 O A:CYS26 4.1 0.0 1.0 N A:CYS55 4.1 0.0 1.0 HB2 A:CYS52 4.2 0.0 1.0 HE1 A:TYR33 4.2 0.0 1.0 CA A:CYS52 4.2 0.0 1.0 HB2 A:CYS29 4.2 0.0 1.0 CA A:CYS55 4.3 0.0 1.0 HB2 A:LYS54 4.3 0.0 1.0 N A:CYS29 4.4 0.0 1.0 CA A:CYS29 4.5 0.0 1.0 CA A:CYS26 4.6 0.0 1.0 C A:CYS26 4.6 0.0 1.0 HA A:ARG51 4.7 0.0 1.0 HA A:CYS55 4.7 0.0 1.0 O A:CYS52 4.7 0.0 1.0 C A:CYS52 4.8 0.0 1.0 C A:CYS29 4.9 0.0 1.0 HB3 A:ARG51 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