Atom Nomenclature for JZN

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 JZN

Atom Name (V3) Atom Name (V2)
C1 C1
F1 F1
N1 N1
O1 O1
C2 C2
F2 F2
N2 N2
O2 O2
C3 C3
F3 F3
N3 N3
O3 O3
C4 C4
F4 F4
N4 N4
O4 O4
C5 C5
N5 N5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
H1 H1
H1A H1A
H1B H1B
HN1 HN1
HO2 HO2
H3 H3
H4 H4
HN5 HN5
HN5A HN5A
H6 H6
H9 H9
H9A H9A
H9B H9B
H10 H10
H10A H10A
H10B H10B
H11 H11
H11A H11A
H13 H13
H13A H13A
H15 H15
H17 H17
H17A H17A
H17B H17B
H18 H18
H20 H20
H23 H23
H24 H24
H25 H25
H27 H27
H29 H29
H29A H29A
H30 H30
H30A H30A
H31 H31
H31A H31A
H32 H32