Modification Summary

2′-O-methylcytidine

[show modification pathway]
Cm

Summary

Full name2′-O-methylcytidine
Short nameCm
New Nomenclature0C
RNAMods abbreviationB
HTML abbreviationB
Enzymes Nop1 (Saccharomyces cerevisiae)
RlmM (Escherichia coli)
RsmI (Escherichia coli)
Trm13 (Saccharomyces cerevisiae)
Trm7 (Saccharomyces cerevisiae)
TrmJ (Escherichia coli)
TrmJ (Sulfolobus acidocaldarius)
TrmL (Escherichia coli)
aTrm56 (Pyrococcus abyssi)
Found in phylogenyEubacteria, Eukaryota
Found in RNArRNA, snRNA, tRNA
PubChem ID150971
SMILES codeC3(OC(CO)C(O)C(O(C))3)N1C=CC(N)=NC1(=O)

LC-MS Information

Sum formulaC10O5N3H15
Monoisotopic mass257.10117
Average mass257.2467
HRMS mass257.100621
Normalized LC elution time *0,90 (Kellner 2014); 0,92 (Kellner 2014)
LC elution order/characteristicsbetween U and G (Kellner 2014, Kellner 2014)
Mass transition-146 (Kellner 2014, Kellner 2014, Su 2014)

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Profiling of RNA modifications by multiplexed stable isotope labelling. Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. Chem Commun (Camb). [details] 24567952 -
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC... Nat Protoc [details] 24625781 -
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Kellner S, Ochel A, Thuring K, Spenkuch F, Neumann J, Sharma S, Entian KD, Schneider D, Helm M... Nucleic Acids Res [details] 25129236 -

Download [.mol file for Cm]

Chemical groups contained

methyl groupmethyl at O2

Reactions producing 2′-O-methylcytidine

Name
C:Cm

Reactions starting from 2′-O-methylcytidine

Name
Cm:m4Cm
Cm:m5Cm
Cm:ac4Cm
Cm:f5Cm

Occurrence in PDB structures

PDB-ID chain residue
1ehz A OMC /32
1evv A OMC /32
1fcw A OMC /32
1fcw B OMC /32
1fcw C OMC /32
1fcw D OMC /32
1fcw E OMC /32
1gix B OMC /32
1gix C OMC /32
1jgo B OMC /32
1jgo C OMC /32
1jgp B OMC /32
1jgp C OMC /32
1jgq B OMC /32
1jgq C OMC /32
1luu A OMC /32
1lux A OMC /32
1mj1 D OMC /32
1mj1 C OMC /32
1ml5 B OMC /32
1nao B OMC /12
1nao B OMC /17
1ob2 B OMC /32
1ob5 B OMC /32
1ob5 D OMC /32
1ob5 F OMC /32
1pbl A OMC /1
1pbl A OMC /3
1pbl A OMC /5
1pbl B OMC /7
1pbl B OMC /9
1pbl B OMC /11
1sz1 E OMC /32
1sz1 F OMC /32
1tn2 OMC /32
1tra OMC /32
1ttt D OMC /32
1ttt E OMC /32
1ttt F OMC /32
2fmt C OMC /32
2fmt D OMC /32
2goz B OMC /6
486d A OMC /32
4tna OMC /32
4tra OMC /32
6tna OMC /32

Last modification of this entry: 2017-07-05 15:38:57.876420
Edited by a user: pboccaletto
Edited content: Changed lc_elution_time, lc_elution_comment, lc_reference and mass_trans.