Atom Nomenclature for BB8

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 BB8

Atom Name (V3) Atom Name (V2)
N N
CA CA
C C
CB CB
OB OB
CG CG
CD1 CD1
CE1 CE1
CZ CZ
CE2 CE2
CD2 CD2
O O
OXT OXT
HN1 HN1
HA2 HA2
HA HA
HB HB
HXT HXT
HC HC
HD1 HD1
HD2 HD2
HE1 HE1
HZ HZ
HE2 HE2