Structural features of the D-loop of BEVSLD

Copyright information:

Taken from "A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA"

Nucleic Acids Research 2005;33(6):2003-2011.

Published online 6 Apr 2005

PMCID:PMC1074726.

© The Author 2005. Published by Oxford University Press. All rights reserved

() The G62:A65 ‘pseudo base pair’ as found in the experimentally determined mean structure of BEVSLDap. () The G62:A65 base pair forming three hydrogen bonds (indicated as broken green lines) as derived from a 4 ns MD simulation using the calculated mean structure of BEVSLDap as starting structure. () Superimposition (backbone atoms of loop and closing base pair, top view) of the apical loop regions of the BEVSLDap structure (nt 61–66, red) with SLD of coxsackievirus B3 (uCACGg, blue, PDB 1RFR) and the TL1 tetraloop from 16S rRNA (cUUCGg, yellow, PDB 1F7Y). () Superimposition (backbone atoms of loop and closing base pair, top view) of the apical loop region of the BEVSLDap structure (nt 61–66, red) with the crystal structure of the cGUAAg tetraloop (blue, PDB 1MSY). The 5′ and 3′ ends of the tetraloop backbones are indicated.