Atom Nomenclature for CIR

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 CIR

Atom Name (V3) Atom Name (V2)
C C1
O O1
OXT O2
CA C2
N N2
C3 C3
C4 C4
C5 C5
N6 N6
C7 C7
O7 O7
N8 N8
HXT HO2
HA H2
H2 HN21
H HN22
H31 H31
H32 H32
H41 H41
H42 H42
H51 H51
H52 H52
HN6 HN6
HN81 HN81
HN82 HN82