computer modeling in molecular biology.pdf

5 Modellinn Nucleic Acids 117Figure 5-7. Example of an “inner” complex between a partially hydrated sodium ion and twonucleic acid fragments (above; adapted from Chevrier et al. [38]) and of an “outer” complexbetween fully hydrated magnesium ions and the deep groove of the anticodon helix (below;from Westhof and Sundaralingam [65]).of water molecules around a sodium or magnesium ion) so that binding can be eitherdue to “outer sphere” complexation (via water molecules) or to “inner sphere” complexation(after removal of one or two water molecules) depending on severalenergetical factors, time scales, and the particular geometry of the nucleic acid. Correctparametrization of such phenomena is by far not available for sodium andmagnesium ions.