Atom Nomenclature for J3Z

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 J3Z

Atom Name (V3) Atom Name (V2)
C2 C2
C4 C4
C5 C5
C6 C6
O1 O1
O3 O3
C7 C7
C8 C8
C9 C9
C10 C10
C12 C12
C3 C3
C14 C14
C15 C15
C16 C16
C21 C21
C17 C17
C18 C18
C19 C19
C20 C20
H2 H2
H14 H14
H24 H24
H16 H16
H26 H26
H36 H36
HO3 HO3
H18 H18
H28 H28
H19 H19
H29 H29
H10 H10
H12 H12
H13 H13
H23 H23
H114 H114
H214 H214
H115 H115
H215 H215
H17 H17
H19A H19A
H20 H20