Primary Citation PubMed: 18455733
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Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs.
(2014) Nucleic Acids Res 42
PubMed: 24121683 | PubMedCentral: PMC3902895 | DOI: 10.1093/nar/gkt800
Motifs (a–e) from PDBs 1EVV, 1YIJ, 1EHZ, 1FFK and 3CCL, respectively.
All computed interactions are reported with the corresponding PDB code and resolution, of the selected crystal structure Motif Occurrency Interaction PDB; Biomolecule Resolution (Å) Crystallographic G:C motif GCC tWW/tSW 9 G15:C48:C20 1H3E; tRNA Tyr 2.90 W:W trans GCU tWW/Intermediate-O4(U) 10 G:515:C548:U520 1N78; tRNA Glu 2.10 W:W trans GCH2U(rG) tWW/tSW 1 G15:C48:H2U20A:G20B 1SER;tRNA Ser 2.90 W:W trans GrCrG tWW/cSS 74 G430:C234:G219 3uz2; 23S rRNA 2.80 W:W trans GGCU(i) tHS/tWW/tWW 17 G1371:G1360:C2214: U2210 1VS8; 23S rRNA 3.50 W:W trans GGCU(ii) tHS/tWW/tWW 5 G1371:G1360:C2214: U2210 3OAS; 23S rRNA 3.25 Ww/Bs trans GGCU(iii) tHS/tWW/tWW 8 G1371:G1360:C2214: U2210 2AW4; 23S rRNA 3.46 Ww/Bw trans GC tWW/wc 160 G15:C48:w916 1EVV; tRNA Phe 2.00 W:W trans GC tWW/wa 82 G1873:C1856:w9741 1YIJ; 23S rRNA 2.60 W:W trans GC tWW/wcwa 68 G15:C48:w104:w121 1EHZ; tRNA Phe 1.93 W:W trans GC tWW/OP1 269 G2564:C2510:PO1 2508 1FFK; 23S rRNA 2.40 W:W trans GC tWW/OP1wc 34 G2564:C2510:PO1(C2508)w3705 3CCL; 23S rRNA 2.90 W:W trans QM calculations A density functional theory approach, based on the hybrid B3LYP functional as implemented in the gaussian09 package ( 47–49 ) and the cc-pVTZ basis set ( 50 ), was used for all geometry optimizations, both in the gas phase and in water, modeled with the continuum polarizable model C-PCM ( 51 , 52 ).
Publication Year: 2014
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