Atom Nomenclature for BAB

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 BAB

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
N1 N1
N2 N2
N3 N3
N4 N4
C1' C1'
C2' C2'
C3' C3'
C4' C4'
C5' C5'
C6' C6'
C7' C7'
C8' C8'
N1' N1'
N2' N2'
N3' N3'
N4' N4'
H2 H2
H3 H3
H6 H6
H91 1H9
H92 2H9
HN21 1HN2
HN22 2HN2
HN4 HN4
H2' H2'
H3' H3'
H6' H6'
H2'1 1H2'
H2'2 2H2'
HN4' 'HN4
HN1 1H1'
HN2 2H1'
HN3 'HN3
HN5 1HN1
HN6 2HN1