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Results: 4

1.
Figure 3

Figure 3. From: Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

(A) Stereo view of the AA1 platform containing RNA fragment and 18 low energy ion binding sites (indicated by crosses) obtained after systematic docking by energy minimisation of ∼800 evenly distributed K+ ions at the surface of the RNA fragment. The three most favourable ion binding positions are indicated by an increased cross thickness. (B) Stereo view of the AA2 platform containing RNA fragment with the 18 most favourable calculated K+ binding sites.

Carmen Burkhardt, et al. Nucleic Acids Res. 2001 October 1;29(19):3910-3918.
2.
Figure 2

Figure 2. From: Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

Plot of the calculated relative ion binding energy versus the reciprocal ion (van der Waals) radius for the (A) AA1- and the (B) AA2-containing RNA fragments with various alkali ions bound at the experimentally observed coordination site. The reciprocal ions radii (x-axis) follow the order Cs+, Rb+, K+, Na+ and Li+, with results for docking to fully flexible RNA represented by dots and for rigid RNA (energy minimised before ion docking in the absence of a bound ion) represented by triangles.

Carmen Burkhardt, et al. Nucleic Acids Res. 2001 October 1;29(19):3910-3918.
3.
Figure 4

Figure 4. From: Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

Calculated relative K+ binding energies of the 18 most favourable ion binding positions obtained from systematic docking studies to RNA fragments containing the AA1 platform (A) and the AA2 platform (B), respectively. The most favourable binding energy (left most bar) was obtained for binding to the experimentally observed coordination site for both platform motifs. Binding energies were calculated by subtracting the ion–RNA complex energy from the energy of the isolated ion and the RNA (rigid RNA, non-polar solvation term not included). Electrostatic solvation contributions were calculated by solving the non-linear FDPB in the absence (continuous lines) and presence of 150 mM bulk salt (dashed lines).

Carmen Burkhardt, et al. Nucleic Acids Res. 2001 October 1;29(19):3910-3918.
4.
Figure 1

Figure 1. From: Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

Stereo views of the superposition of AA platform containing RNA fragments (continuous line) energy minimised with a bound K+ ion (indicated as a sphere) at a position compatible with the experimentally observed coordination geometry (8) onto the corresponding crystallographic Tetrahymena ribozyme P4-P6 domain structure (PDB accession no. 1gid, reference 5, dashed line). (A) RNA fragment with the AA1 platform corresponding to nucleotides 221–229 (first strand) and 245–252 (second strand), respectively. (B) AA platform 2 (AA2) containing fragment (continuous line) with a bound K+ superimposed on nucleotides 215–223 (first strand), nucleotides 103–105 (second strand pairing with nucleotides 215–217) and nucleotides 250–253 (third strand, pairing with nucleotides 220–223 of the first strand) from the crystal structure (dashed line).

Carmen Burkhardt, et al. Nucleic Acids Res. 2001 October 1;29(19):3910-3918.

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