Sandbox Reserved 1649: Difference between revisions

LBD is constituted of two domains S1 (located juste upstream M1 transmembrane domain) and S2 and has affinity for <scene name='86/868182/Lbd/3'>glutamate</scene> or sometimes [https://en.wikipedia.org/wiki/Glycine Glycine]. Positive charge of amino-group of the agonist binds to negative charges residue of the pocket D731. In [https://proteopedia.org/wiki/index.php/Glutamate_receptor_%28GluA2%29 GlurR], negative charge amino acid is a E731 and is able to form salt bridge with agonist. In NR2A D731 (which corresponds to <scene name='86/868182/D213/3'>D213</scene>) is not able to do salt bridge with amino group because aspartate is one methylene lacking to do it. Amino group of agonist is stabilized by water mediated hydrogen bonds to amino acid Y761 (which corresponds to <scene name='86/868182/Y243/2'>Y243</scene>) and E413 (which correspond to <scene name='86/868182/E14/3'>E14</scene>).<scene name='86/868182/Y243_et_e14/2'>Click here if you want to see E14 and Y243 together</scene>. The high affinity for glutamate agonist may be because of Van der Walls contact between γ-carboxylate group of glutamate and Y730 of S2 domain which is conserved in NR2 protein.<ref name="LBD">DOI 10.1038/nature04089</ref> Amino-group of glutamate also interacts with <scene name='86/868182/T114/3'>T114</scene> and <scene name='86/868182/S112/2'>S112</scene>. <scene name='86/868182/T114_et_s112/2'>(T114 and S112 together).</scene>