Atom Nomenclature for Z57

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 Z57

Atom Name (V3) Atom Name (V2)
C1A C1
O1 O1
C2A C2
C3A C3
C4A C4
O4A O4
C5A C5
BR5 BR5
C6A C6
C1 C1'
C2 C2'
O2 O2'
C3 C3'
O3 O3'
C4 C4'
O4 O4'
C5 C5'
O5 O5'
C6 C6'
O6 O6'
HO1 HO1
H3A H3
HO4A HO4
H6 H6
H1 H1'
H2 H2'
HO2 HO2'
H3 H3'
HO3 HO3'
H4 H4'
HO4 HO4'
H5 H5'
H61 H6'
H62 H6'A
HO6 HO6'