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Table 4 Comparison of frequency of A minor motif interactions and Mg2+ binding in the vicinity of the reactive and unreactive nucleotide pairs

From: Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome

UV reactions

Nucleotide Pairs

 

Statistics1

 

Parameter

Reactive

Unreactive

z value

p value

Number of nt. pairs in A minor motif2

0 of 14 nt. pairs

31 of 1388 nt. pairs

-0.5998

0.549

Mg2+ in vicinity of nt.3

54 Mg2+ at 56 nt.

613 Mg2+ at 698 nt.

0.2324

0.816

Mg2+ bridges in vicinity of nt. pair4

2 of 28 nt. pairs

131 of 4312 nt. pairs

1.1695

0.242

UVA-s 4 U reactions

Nucleotide Pairs

 

Statistics

 

Parameter

Reactive

Unreactive

z value

p value

Number of nt. pairs in A minor motif5

0 of 18 nt. pairs

9 of 1868 nt. pairs

-0.3007

0.764

Mg2+ in vicinity of nt.6

31 Mg2+ at 54 nt.

3034 Mg2+ at 3660 nt.

-0.9186

0.359

Mg2+ bridges in vicinity of nt. pair7

1 of 36 nt. pairs

71 of 5522 nt. pairs

0.7528

0.452

  1. 1 z-value is the difference of sample means normalized by the standard error of the means. The null hypothesis, that the populations have the same averages, can be rejected at the 5% and 1% level of significance if |z| ≥ 1.96 and |z| ≥ 2.56, respectively. p-value is the probability that random sampling would lead to a difference between sample means as large (or larger) than that has been observed, if the null hypothesis is true, i.e., if the populations have the same true mean.
  2. 2Sixteen nucleotide pairs in observed crosslinks and 671 and 712 nucleotide pairs at unreactive sites in the E. coli I and II structures [13] were evaluated using the list of A minor motif interactions [31].
  3. 3Twenty nine nucleotides from the observed UV crosslinks and 698 randomly selected nucleotides from the list of unreactive nucleotide pairs in the T. thermophilus [11] and E. coli I and II structures [13] were evaluated using the lists of Mg2+ interaction in the T. thermophilus I and II structures [34].
  4. 4Fifteen nucleotide pairs in observed crosslinks and 2156 nucleotide pairs at unreactive sites in the T. thermophilus [11] and E. coli I and II [13] structures were evaluated using the lists of the Mg2+ interactions sites in the T. thermophilus I and II structures [34].
  5. 5Eighteen nucleotide pairs in observed crosslinks and 928 and 940 nucleotide pairs at unreactive sites in the E. coli I and II structures [13] were evaluated using the list of A minor motif interactions [31].
  6. 6Twenty seven nucleotides from the observed UVA-s4U crosslinks and 3660 randomly selected nucleotides from the list of unreactive nucleotide pairs in the T. thermophilus [11] and E. coli I and II structures [13] were evaluated using the lists of Mg2+ interaction in the T. thermophilus I and II structures [34].
  7. 7Eighteen nucleotide pairs in observed crosslinks and 2761 nucleotide pairs at unreactive sites in the T. thermophilus [11] and E. coli I and II [13] structures were evaluated using the lists of the Mg2+ interactions sites in the T. thermophilus I and II structures [34].
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BMC Structural Biology

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