Atom Nomenclature for RBZ

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 RBZ

Atom Name (V3) Atom Name (V2)
N3 N3
N1 N1
C2 C2
C7A C7A
C3A C3A
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
P P
O1P O1P
O2P O2P
O3P O3P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
O2' O2*
C1' C1*
H2 H2
H4 H4
H7 H7
H81 1H8
H82 2H8
H83 3H8
H91 1H9
H92 2H9
H93 3H9
HOP2 2HOP
HOP3 3HOP
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
HO'3 3HO*
H2' H2*
HO'2 2HO*
H1' H1*