What is an aromatic cage and what does it do?
It refers to the structures in the PHD-finger domain and chromodomains. The aromatic amino acid residues form a cage like structure which covers and interacts with the methylated ammonium of lysine via a cation-pi interaction.


  The BPTF-PHD structures reveal the main characteristics of PHD fingers that can read H3K4me3. The binding occurs through an aromatic cage where a trimethyl ammonium group is stabilized by van der Waals and cation-–π interaction, which is similar to the ones observed in chromodomain, MBT, PWWP, and Tudor domains. This aromatic cage is composed of one Trp and three Tyr residues; and it has three faces and a 'lid' that is beyond the tip of H3K4me3. Subsequently determined structures of other fingers in complex with the H3K4me3 peptides show that the cage varies and can contain a combination of two to four aromatic and hydrophobic residues. 



 Margueron et al., 2009