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. 2006 Feb 2;34(2):697–708. doi: 10.1093/nar/gkj470

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© The Author 2006. Published by Oxford University Press. All rights reserved

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Hydration and ion-binding sites observed in MD simulations. Ions and water molecules (only oxygens are shown) are black and orange balls, respectively. (A) Tetraloop area—ion positioned near N7(G2659), waters at IIa, IIb and IId positions, (B) ECOLI flexible region—ions near O4(U2653) and N7(G2668); waters at IV, IVac, IVuc and V sites.