Atom Nomenclature for M33

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 M33

Atom Name (V3) Atom Name (V2)
PB PB
O1B O1B
O2B O2B
C3B C3B
PA PA
O1A O1A
O2A O2A
O3A O3A
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
O2' O2'
C1' C1'
N9 N9
C8 C8
N7 N7
C5 C5
C6 C6
N6 N6
N1 N1
C2 C2
N3 N3
C4 C4
HO2B HO2B
H3B1 1H3B
H3B2 2H3B
H3B3 3H3B
HO1A HO1A
H5'1 1H5'
H5'2 2H5'
H4' H4'
H3' H3'
HO3' HO3'
H2' H2'
HO2' HO2'
H1' H1'
H8 H8
HN61 1HN6
HN62 2HN6
H2 H2