Atom Nomenclature for M7G

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for M7G

Atom Name (V3) Atom Name (V2)
PA PA
O1A O1A
O2A O2A
O3A O3A
O5' O5'
PB PB
O1B O1B
O2B O2B
O3B O3B
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
O2' O2'
C1' C1'
N9 N9
C8 C8
N7 N7
CM7 CM7
C5 C5
C6 C6
O6 O6
N1 N1
C2 C2
N2 N2
N3 N3
C4 C4
HOA2 HOA2
HOB2 HOB2
HOB3 HOB3
H5'1 H5'1
H5'2 H5'2
H4' H4'
H3' H3'
HO3' HO3'
H2' H2'
HO2' HO2'
H1' H1'
H81 H81
HM71 HM71
HM72 HM72
HM73 HM73
HN1 HN1
HN21 HN21
HN22 HN22