Different names for the methyl group in DNA and RNA structures

Recently I was a bit surprised to find that the methyl group is named differently in the PDB: C7 in DT8 (thymine) of B-DNA 355d, CM5 in 5MC40 (5-methylated C) of tRNA 1ehz, and C5M in 5MU54 (5-methylated U, i.e., T) of the same tRNA 1ehz. See the three figures below for details.

I know that the previously named C5M of thymine in DNA has been renamed C7 as a result of the 2007 remediation effort (PDB v3). However, browsing through the wwPDB Remediation website and reading carefully the article Remediation of the protein data bank archive, I failed to see explanations of the obvious inconsistency of CM5 (5MC40) vs C5M (5MU54) in the nomenclature of the 5-methyl group in the same tRNA entry 1ehz, except for the following note:

As with the Chemical Component Dictionary, names for standard amino acids and nucleotides follow IUPAC recommendations (10) with the exception of the well-established convention for C-terminal atoms OXT and HXT. These nomenclature changes have been applied to standard polymeric chemical components only.

5-methyl is named C7 in DT8 of the DNA entry 355d

5-methyl in DT8 is named C7 in DNA (355d)

5-methyl is named CM5 in 5MC40 of the RNA entry 1ehz

5-methyl in 5MC40 is named CM5 in RNA (1ehz)

5-methyl is named C5M in 5MU54 of the RNA entry 1ehz

5-methyl in 5MU54 named C5M in RNA (1ehz)

Am I missing something obvious? If you have any further information, please leave a comment. Whatever the case, it helps (at least won’t hurt) to know the naming discrepancy for those who care about the small methyl group in nucleic acid structures.





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