new group for phosphorothioate DNA #53
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Contributor
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I think SDNA/SRNA would be workable |
keitaroyam
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Apr 10, 2024
Contributor
Author
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Do you mean SDNA/RNA? SDNA/SRNA is too wide (9 letters) and Refmac cannot handle it (and won't fit the PDB format). |
Contributor
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Ok. Then you can have: SDNA/RNA, you could also have SDNA, SRNA (I think current CCD has these) |
Contributor
Author
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Yes, but we don't need to separate them, unless we need a link around O2'. For now we do have DNA, RNA and DNA/RNA. This is a bit confusing.. |
Contributor
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I understand. Unless in the current mechanism we remove RNA and DNA, keep only RNA/DNA you could also have the same mechanism for SDNA and SRNA |
Contributor
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What is happening with this addition? |
Contributor
Author
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I just need to find time to finalise this |
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Phosphorothioate DNA is a modified DNA where the OP2 atom is substituted with sulfur (S2P); for example: AS PST GS SC. I would like to have a new group for this kind of monomers, to make refinement easier.
There are some inconsistencies in the CCD. In AS, there is P=S double bond, while in GS it's P-SH single bond. I fixed P-SH type monomers: 1SC 48Z 6NW 6OO C7R C7S DV3 F2T G46 GS OKN OKQ OKT U37 YA4. Hopefully CCD will accept these fixes (haven't ask yet).
I don't know if "S-NA" is a good name - should it be "SDNA/RNA", or any alternative? We can proceed once we decide a name for this new group.