Sandbox Z-DNA: Difference between revisions
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== Comparison of the three helices and helical parameters of DNA == | == Comparison of the three helices and helical parameters of DNA == | ||
<applet load='A-DNA_ali.pdb' size=' | ''Sources''<ref>PMID: 19417072</ref> | ||
<applet load='B-DNA_ali.pdb' size=' | |||
<applet load='Z-DNA_ali.pdb' size=' | <applet load='A-DNA_ali.pdb' size='350' frame='true' align='right' caption='A-DNA' align='left' scene ='Sandbox_Z-DNA/A-dna_ali/1'/> | ||
<applet load='B-DNA_ali.pdb' size='350' frame='true' align='right' caption='B-DNA' align='left' scene ='Sandbox_Z-DNA/B-dna_ali/1'/> | |||
<applet load='Z-DNA_ali.pdb' size='350' frame='true' align='right' caption='Z-DNA' align='left' scene ='Sandbox_Z-DNA/Z-dna_ali/1'/> | |||
<jmol> | <jmol> | ||
<jmolRadioGroup> | <jmolRadioGroup> | ||
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<script>sync* OFF</script> | <script>sync* OFF</script> | ||
<text>Unsynchronize </text> | <text>Unsynchronize </text> | ||
</item> | |||
</jmolRadioGroup> | </jmolRadioGroup> | ||
</jmol> | </jmol> | ||
{| class="wikitable" align= "center'' | |||
{| class="wikitable" align='' | |||
|- | |- | ||
!Parameter | !Parameter | ||
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|Residues per turn ||align="right"| 11 ||align="right"| 10.5 ||align="right"| 12 | |Residues per turn ||align="right"| 11 ||align="right"| 10.5 ||align="right"| 12 | ||
|- | |- | ||
|Axial rise | |Axial rise [Å] ||align="right"| 2.55 ||align="right"| 3.4 ||align="right"| 3.7 | ||
|- | |- | ||
|Helix pitch(°) ||align="right"| 28 ||align="right"| 34 ||align="right"| 45 | |Helix pitch(°) ||align="right"| 28 ||align="right"| 34 ||align="right"| 45 | ||
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|Rotation per residue (°) ||align="right"| 33||align="right"| 36||align="right"|-30 | |Rotation per residue (°) ||align="right"| 33||align="right"| 36||align="right"|-30 | ||
|- | |- | ||
|Diameter of helix | |Diameter of helix [Å]||align="right"| 23||align="right"| 20||align="right"| 18 | ||
|- | |- | ||
|Glycosidic bond configuration<br\>dA,dT,dC<br\>dG ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>syn | |Glycosidic bond configuration<br\>dA,dT,dC<br\>dG ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>anti ||align="center"| <br\>anti<br\>syn | ||
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|Sugar pucker<br\>dA,dT,dC<br\>dG ||align="center"| <br\>C3'-endo<br\>C3'-endo ||align="center"|<br\> C2'-endo<br\>C2'-endo ||align="center"| <br\>C2'-endo<br\>C3'-endo | |Sugar pucker<br\>dA,dT,dC<br\>dG ||align="center"| <br\>C3'-endo<br\>C3'-endo ||align="center"|<br\> C2'-endo<br\>C2'-endo ||align="center"| <br\>C2'-endo<br\>C3'-endo | ||
|- | |- | ||
|Intrastrand phosphate-phosphate distance | |Intrastrand phosphate-phosphate distance [Å] <br\>dA,dT,dC<br\>dG ||align="center"| <br\>5.9<br\>5.9||align="center"| <br\>7.0<br\>7.0||align="center"| <br\>7.0<br\> 5.9 | ||
|- | |- | ||
|colspan="4"|''Sources:<ref name="Rich1984">PMID:6383204</ref><ref name="Rich1979">PMID: 514347</ref><ref> Sinden, Richard R (1994-01-15). ''DNA structure and function'' (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.</ref> | |colspan="4"|''Sources:<ref name="Rich1984">PMID:6383204</ref><ref name="Rich1979">PMID: 514347</ref><ref> Sinden, Richard R (1994-01-15). ''DNA structure and function'' (1st ed.). Academic Press. pp. 398. ISBN 0-12-645750-6.</ref> | ||