Atom Nomenclature for BSP

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 BSP

Atom Name (V3) Atom Name (V2)
C5 C5
C4 C4
C3 C3
C8 C8
C7 C7
C6 C6
BR6 BR6
BR7 BR7
BR5 BR5
BR4 BR4
C9 C9
O1 O1
O9 O9
C2 C2
C1' C1'
C2' C2'
C3' C3'
C4' C4'
C5' C5'
C6' C6'
O4' O4'
S1' S1'
OS1 OS1
OS2 OS2
OS3 OS3
C1B C1*
C2B C2*
C3B C3*
C4B C4*
C5B C5*
C6B C6*
O4B O4*
S1B S1*
OSA OSA
OSB OSB
OSC OSC
H2' H2'
H5' H5'
H6' H6'
H4' H4'
H2B H2*
H5B H5*
H6B H6*
H4B H4*