Atom Nomenclature for C96

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 C96

Atom Name (V3) Atom Name (V2)
O4 O4
S2 S2
O3 O3
N6 N6
C16 C16
C15 C15
C14 C14
C13 C13
C18 C18
C17 C17
C4 C4
O2 O2
C3 C3
C2 C2
C1 C1
C6 C6
C7 C7
S1 S1
C9 C9
N3 N3
N2 N2
C8 C8
C20 C20
O1 O1
H6N1 1H6N
H6N2 2H6N
H17 H17
H15 H15
H18 H18
H14 H14
H3 H3
H2 H2
H201 1H20
H202 2H20
H203 3H20
H3N1 1H3N
H3N2 2H3N