Atom Nomenclature for BIO

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 BIO

Atom Name (V3) Atom Name (V2)
N1 N1
N2 N2
C2 C2
N3 N3
C4 C4
O4 O4
C4A C4A
C8A C8A
N8 N8
C7 C7
C6 C6
N5 N5
C9 C9
O9 O9
C10 C10
O10 O10
C11 C11
HN21 1HN2
HN22 2HN2
H3 H3
H7 H7
H9 H9
HO9 HO9
H10 H10
HO1 HO1
H111 1H11
H112 2H11
H113 3H11