Sugar ring pucker: Difference between revisions

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Karsten Theis

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 ==Conformations of ribose rings==
-The two most common conformations are C3' endo and C2' endo. For ribose, endo refers to the side of the glycosidic bond (i.e. the direction of the nucleobase in nucleosides). It is also the direction of the 5'-OH group, whereas the 2'-OH and the 3'-OH are on the exo side. The animation shows a morph between a <jmol><jmolLink><script>script /scripts/90/900784/Endo_exo/2.spt; anim on;</script><text>C3'-endo and a C2'-endo</text></jmolLink> </jmol> conformation. Use the buttons to toggle groups attached to the robise ring. Note how the distance between the 5'-OH and 3'-OH groups (or that of the attached phosphates, if displayed) changes when the conformation changes.
+The two most common conformations are C3' endo and C2' endo. For ribose, endo refers to the side of the glycosidic bond (i.e. the direction of the nucleobase in nucleosides). It is also the direction of the 5'-OH group, whereas the 2'-OH and the 3'-OH are on the exo side. The animation shows a morph between a <jmol><jmolLink><script>script /scripts/90/900784/Endo_exo/3.spt; anim on; ppdiaCaptionCmd = "changeCaption('Different conformations of deoxyribose, the sugar in DNA. The 5 prime carbon defines the endo side, while the oxygen attached to carbon 3 prime is always on the exo side. Depending on the conformation of the ring, either 2 or 3 prime carbon are in an endo position. Coordinates are from 1BNA and 1M77, nucleotide 4.','white','black');";javascript @ppdiaCaptionCmd;</script><text>C3'-endo and a C2'-endo</text></jmolLink> </jmol> conformation. Use the buttons to toggle groups attached to the robise ring. Note how the distance between the 5'-OH and 3'-OH groups (or that of the attached phosphates, if displayed) changes when the conformation changes.
 <jmol>