Atom Nomenclature for CVR

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 CVR

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
N3 N3
C4 C4
C5 C5
C6 C6
N6 N6
N7 N7
C8 C8
N9 N9
PA PA
PB PB
C1' C1'
O1A O1A
O1B O1B
C1D C1D
C2' C2'
O2' O2'
O2A O2A
O2B O2B
C2D C2D
O2D O2D
C3' C3'
O3' O3'
O3A O3A
C3D C3D
O3D O3D
C4' C4'
O4' O4'
C4D C4D
C4X C4X
C5' C5'
O5' O5'
C5D C5D
O5D O5D
H2 H2
HN6 HN6
H8 H8
H1' H1'
HO1A HO1A
H1D H1D
H2' H2'
HO2' HO2'
HO2B HO2B
H2D H2D
HO2D HO2D
H3' H3'
HO3' HO3'
H3D H3D
HO3D HO3D
H4' H4'
H4D H4D
H4X H4X
H4XA H4XA
H5' H5'
H5'A H5'A
H5D H5D
H5DA H5DA