Atom Nomenclature for X02

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 X02

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
N4 N4
C5 C5
N6 N6
C7 C7
C8 C8
S9 S9
N10 N10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
O18 O18
H1 H1
H1A H1A
H2 H2
H3 H3
H3A H3A
HN4 HN4
HN10 HN10
HN1A HN1A
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17