Sandbox 14

{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition0/1 }}

Molecular Recognition in SelB

Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms

<scene name='Sandbox_14/1wsu-recognition1/4'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene>

The planar base is also sandwiched between

<scene name='Sandbox_14/1wsu-recognition2/2'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a

<scene name='Sandbox_14/1wsu-recognition3/1'>spacefilling diagram.</scene>

The overall shape of the hairpin is recognized by contacts with several

<scene name='Sandbox_14/1wsu-recognition4/1'>arginine and lysine amino acids.</scene>

In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of

<scene name='Sandbox_14/1wsu-recognition5/1'>arginine 606.</scene>