Atom Nomenclature for OAG

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 OAG

Atom Name (V3) Atom Name (V2)
C1 C1
N1 N1
CL2 CL2
CL5 CL5
C9 C9
C1' C1*
N1' N1*
C10 C10
C11 C11
C12 C12
C2' C2*
N2' N2*
C3' C3*
N3' N3*
C4' C4*
N4' N4*
C4A C4A
C5' C5*
C6' C6*
C7' C7*
N8' N8*
C8A C8A
H1 H1
H1A H1A
HN1 HN1
H9 H9
H12 H12
HN2' HN2*
HN2A HN2A
H3' H3*
HN4' HN4*
HN4A HN4A
H6' H6*
H7' H7*