Atom Nomenclature for BTS

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 BTS

Atom Name (V3) Atom Name (V2)
C5 C5
C4 C4
C6 C6
N3 N3
C2 C2
S1 S1
C7A C7A
C3A C3A
C7 C7
S2 S2
C1 C1
C8 C8
C9 C9
S3 S3
O2 O2
O3 O3
O4 O4
H5 H5
H4 H4
H6 H6
H7 H7
H11 1H1
H12 2H1
H81 1H8
H82 2H8
H91 1H9
H92 2H9
HO4 HO4