Atom Nomenclature for C2U

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 C2U

Atom Name (V3) Atom Name (V2)
O7B O7B
C7 C7
O7A O7A
C6 C6
C1 C1
C5 C5
O5 O5
C4 C4
CL4 CL4
C3 C3
C2 C2
CL2 CL2
HO7B HO7B
H1 H1
HO5 HO5
H3 H3