Sandbox 201: Difference between revisions
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:The enzyme binds <scene name='Sandbox_201/Mg/1'>two magnesium ions</scene> Mg<sup>2+</sup>. The true substrate in the adenylation reaction is the ATP-Mg<sup>2+</sup> complex, <ref>Cherepanov, A. V., and de Vries, S. (2002) J. Biol. Chem. 277, 1695–1704</ref> but nucleotidyltransferase enzymes cannot bind ATP-Mg<sub>2</sub> directly. They bind ATP-Mg first, then a second Mg<sup>2+</sup> ion. Each oh these cations <scene name='Sandbox_201/Mg_apc_residues/2'>interact via hydrogen bonds</scene> with one phosphoryl oxygen from AMPcPP, three water molecules and two residues (Gly269 and Asp272), which both belong to the C-terminal domain. | :The enzyme binds <scene name='Sandbox_201/Mg/1'>two magnesium ions</scene> Mg<sup>2+</sup>. The true substrate in the adenylation reaction is the ATP-Mg<sup>2+</sup> complex, <ref>Cherepanov, A. V., and de Vries, S. (2002) J. Biol. Chem. 277, 1695–1704</ref> but nucleotidyltransferase enzymes cannot bind ATP-Mg<sub>2</sub> directly. They bind ATP-Mg first, then a second Mg<sup>2+</sup> ion. Each oh these cations <scene name='Sandbox_201/Mg_apc_residues/2'>interact via hydrogen bonds</scene> with one phosphoryl oxygen from AMPcPP, three water molecules and two residues (Gly269 and Asp272), which both belong to the C-terminal domain. | ||
:The enzyme binds <scene name='Sandbox_201/Ca/1'>four calcium ions</scene> Ca<sup>2+</sup>. <scene name='Sandbox_201/Ca6_apc_residues/ | :The enzyme binds <scene name='Sandbox_201/Ca/1'>four calcium ions</scene> Ca<sup>2+</sup>. <scene name='Sandbox_201/Ca6_apc_residues/2'>Two</scene> are coordinated to six water molecules. They do not directly interact with the enzyme, but via water molecules interacting with Glu227, Glu159, Lys99, Glu100, and Tyr246 via hydrogen bonds. They also interact with one phosphoryl oxygen of the AMPcPP. <scene name='Sandbox_201/Ca4_residues/3'>Two other</scene> are coordinated to four water molecules and interact with three enzyme residues (Ile211 and Asp212) via hydrogen bonds. | ||
:Calcium is very important for enzyme Rnl1 structural biology, because the enzyme crystallizes only in présence of Ca<sup>2+</sup>. This could be explained by the fact that interactions between Ca<sup>2+</sup> and negatively charged surface of each Rnl1 allow interactions between several enzymes at crystallization interfaces.<ref name="main_article" /> | :Calcium is very important for enzyme Rnl1 structural biology, because the enzyme crystallizes only in présence of Ca<sup>2+</sup>. This could be explained by the fact that interactions between Ca<sup>2+</sup> and negatively charged surface of each Rnl1 allow interactions between several enzymes at crystallization interfaces.<ref name="main_article" /> | ||
