 | Acta Crystallographica Section D Acta Crystallographica Section D BIOLOGICAL CRYSTALLOGRAPHY |
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![[Figure 4]](hm5049fig4mag.jpg)
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Figure 4
Comparison of the local structural effects of the synthetic C3L and S9L residues observed in the hinge region between the loop A and B domains. (a) σA-Weighted simulated-annealing mFo − DFc omit electron-density map calculated for the C3L residue and flanking G15 phosphate. Blue density is contoured at 3σ and green density at 9σ. The distance between atom O3′ of residues 13 and 15 is shown as a dashed line. (b) Omit map for the S9L residue as described in (a); blue density is contoured at 3.5σ and green density at 15σ. (c) Linker and neighboring ribose positions as observed in the superposition of four alternatively hinged hairpin-ribozyme structures. Note the trend in the ribose positions of residue 13 compared with 16. The C3L structure (blue) most closely mimics the natural A14 linkage of the 4WJ structure (salmon), whereas the S9L structure (magenta) most closely mimics the junctionless structure (green). Bases are omitted for clarity, with the exception of A14. (d) Structural influence of the C3L structure on the terminus of H3. The C3L structure is depicted by blue sticks and the S9L structure by magenta lines. The lateral shift of the H3 terminal base pair is represented by the 2.8 Å distance between the O3′ atoms of residue C49 in the respective C3L and S9L structures. The 21 pseudo-helical base-stacking interaction with H4′ is shown to demonstrate the more flush base-stacking interaction exhibited by the C3L structure compared with S9L. The 2.9 Å distance between the O4′ and O3′ atoms of ribose moieties engaged in crystal packing in the C3L structure is compared with the equivalent distances of 3.5 and 4.0 Å displayed for the S9L structure in (e). (e) The equivalent region in the S9L structure, as described in (d). S9L residues are shown as magenta sticks and C3L residues as blue lines. Equivalent O4′–O3′ distances between the H3 and H4′ helices are longer in the S9L structure, which is representative of a more staggered base-stacking interaction. (f) A superposition of the terminal H4 base pair of the C3L and S9L structures demonstrates the influence of the shortened linker on pseudo-helical base stacking. The more flush base stack in the C3L structure is necessarily accompanied by a 1.5 Å upward shift of U31′ to avoid a steric clash with the symmetry-related C49 residue. Note that even after this movement U31′ and C49 are still closer in the C3L structure (d and e). |
![[Figure 4]](hm5049fig4.jpg)
| BIOLOGICAL CRYSTALLOGRAPHY |
ISSN: 1399-0047
