Atom Nomenclature for QSO

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 QSO

Atom Name (V3) Atom Name (V2)
C2 C2
C4 C4
O4 O4
C4A C4A
C8A C8A
C7 C7
C6 C6
C5 C5
C8 C8
C3 C3
O1 O1
C1' C1'
O2 O2
C2' C2'
C3' C3'
C4' C4'
C5' C5'
C6' C6'
O5 O5
O3 O3
CM CM
H2 H2
HO4 HO4
H6 H6
H8 H8
H2' H2'
H3' H3'
H5' H5'
H6' H6'
HO3 HO3
HM1 HM1
HM2 HM2
HM3 HM3