Atom Nomenclature for C9J

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 C9J

Atom Name (V3) Atom Name (V2)
C4 C1
C5 C2
C6 C3
N1 N1
C7 C4
C8 C5
N2 N2
C9 C6
C10 C7
C11 C8
C12 C9
N3 N3
C13 C10
C14 C11
C15 C12
N4 N4
N N5
C C13
O O1
C1 C14
C16 C15
C2 C16
C3 C17
F F1
O1 O2
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12