Atom Nomenclature for BZB

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 BZB

Atom Name (V3) Atom Name (V2)
B B
O1 O1
O2 O2
C1 C1
C2 C2
C8 C8
C3 C3
C7 C7
S S
C4 C4
C6 C6
C5 C5
HO11 1HO1
HO21 1HO2
HC21 1HC2
HC71 1HC7
HC41 1HC4
HC61 1HC6
HC51 1HC5