User:Elizabeth Cook/Sandbox 1: Difference between revisions

Bromodomains are composed of 4 alpha helices (<scene name='10/1079536/Helix/1'>αZ, αA, αB, αC)</scene>, and 2 loops (ZA and BC). There are typically 4 conserved water molecules found within the acetyllysine binding pocket of the bromodomain. The two loops contain the majority of the residues responsible for ligand coordination, including the <scene name='10/1079536/N514_part_2/1'>conserved asparagine</scene> located in the BC loop. In addition, there is a hydrophobic shelf found before the before the ZA loop and following αZ helix. There is also a <scene name='10/1079536/Gatekeeper/1'>gatekeeper residue</scene> that corresponds to the first residue found in the αC that is usually hydrophobic. Histone acetyllysines form a hydrogen bond with the conserved asparagine of bromodomains while various other residues make polar contacts to stabilize the interaction, directly or indirectly.