Atom Nomenclature for ABM

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 ABM

Atom Name (V3) Atom Name (V2)
P P
CM CM
O2P O2P
O3P O3P
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
HM1 HM1
HM2 HM2
HM3 HM3
HOP3 3HOP
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