Atom Nomenclature for A3P

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 A3P

Atom Name (V3) Atom Name (V2)
P1 P1
O1P O1P
O2P O2P
O3P O3P
P2 P2
O4P O4P
O5P O5P
O6P O6P
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
HOP2 2HOP
HOP3 3HOP
HOP5 5HOP
HOP6 6HOP
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
H2' H2*
HO2' *HO2
H1' H1*
H8 H8
HN61 1HN6
HN62 2HN6
H2 H2