Atom Nomenclature for KZI

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 KZI

Atom Name (V3) Atom Name (V2)
O1 O1
O2 O2
O3 O3
N4 N4
N5 N5
N6 N6
N8 N8
N9 N9
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
N42 N42
HN5 HN5
HN6 HN6
HN6A HN6A
HN9 HN9
H10 H10
H11 H11
H11A H11A
H12 H12
H15 H15
H16 H16
H20 H20
H21 H21
H21A H21A
H21B H21B
H24 H24
H25 H25
H25A H25A
H26 H26
H26A H26A
H27 H27
H27A H27A
H27B H27B
H28 H28
H28A H28A
HN42 HN42
HN4A HN4A