Interactions which are absent in a given crystal structure are marked with "-----." Interactions which are present in a given structure are marked with the observed conformation: CO-NH2, C:A carbonyl-amino; imino, A:G imino; N1-NH2, A:A N1-amino; N7-NH2, G:A N7-amino; Wb, wobble pairing.; WC, Watson-Crick
  30S Ribosomal Complex
Pos #s (NT) 1 Native 2 Paromomycin 3 IF1 4 tRNA/mRNA 5
1399:1504 (C:G) WC WC WC WC
1401:1501 (G:C) WC WC WC WC
1402:1500 (C:A) Wb Wb Wb Wb
1404:1497 (C:G) WC WC WC WC
1405:1496 (G:C) WC WC WC WC
1406:1495 (U:U) Wb Wb Wb Wb
1407:1494 (C:G) WC WC WC WC
1408:1493 (A:A) N1-NH2 ----- ----- -----
1409:1492 (C:A) CO-NH2 ----- ----- -----
1491:1492 (G:A) N7-NH2 ----- ----- -----
1409:1491 (C:G) WC WC WC WC
1410:1490 (G:C) WC WC WC WC
1411:1489 (C:G) WC WC WC WC
1412:1488 (C:G) WC WC WC WC
1413:1487 (A:G) imino imino ----- imino
1492-1493 (A-A)        
      stacked yes yes no no
      orientation 6 A B C B
coaxial stack 7 yes yes yes yes
      bend angle 19.68 27.42 25.35 17.56
      displacement 4.33 4.60 1.80 2.88

  1. Pos #s: position numbers, using E. coli (GenBank Accession J01695) numbering. NT: nucleotides present in the T. thermophilus (GenBank Accession #M) crystal structures.
  2. PDB ID 1FJF: Wimberly et al., 2000.
  3. PDB ID 1FJG: Carter et al., 2000.
  4. PDB ID 1HR0: Carter et al., 2001.
  5. PDB ID 1IBM: Ogle et al., 2001.
  6. Orientation of positions 1492-1493: A) staying within the helix boundaries and not interacting with proteins. B) flipped out, extending out of helix, and not interacting with proteins. C) flipped out, extending out of helix, and interacting with the protein IF1.
  7. Coaxial stacking data was determined using Curves (Lavery & Sklenar, 1988, 1989).