Atom Nomenclature for Q3C

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 Q3C

Atom Name (V3) Atom Name (V2)
O13 O13
C11 C11
O12 O12
C7 C7
C3 C3
C9 C9
N5 N5
C2 C2
C6 C6
C10 C10
C8 C8
C4 C4
C1 C1
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7