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![[Figure 7]](qn5003fig7mag.jpg)
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Figure 7
YkoY–alx riboswitch chimera bound to cadmium (PDB entry 6cc1) coloured by the mean Z-score of the simple parameters (ZbpG), illustrating the effects of the use of nucleic acid restraints in PDB-REDO. (a) Structure model as obtained from the PDB. Base-pair atoms are only displayed for pairs with ZbpG > 3.0. (b) Structure model from PDB-REDO. Base-pair atoms are only displayed for pairs with ZbpG > 3.0. (c) Binding site of B/203Cd in the PDB model. The ion is coordinated (thin dotted lines) by seven ligands including the OP1 and OP2 atoms of B/44A. 2mFo − DFc density map in blue at 2.0σ, mFo − DFc difference map in green and red at 3.0σ. For clarity, maps were oversampled with grid size 0.5. (d) The same binding site in the PDB-REDO model. The ion is now coordinated by six ligands as the OP2 atom of B/44A is reoriented towards O2′ of B/41A to form a hydrogen bond (thick dotted lines). |
![[Figure 7]](qn5003fig7.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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