Atom Nomenclature for IZB

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 IZB

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
N4 N4
S5 S5
O6 O6
O7 O7
O9 O9
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C21 C21
C22 C22
N45 N45
S1 S1
O1 O1
O2 O2
C17 C17
C19 C19
C23 C23
C4 C4
C5 C5
C6 C6
N11 N11
C25 C25
N13 N13
C18 C18
O3 O3
C24 C24
C26 C26
N5 N5
C27 C27
C7 C7
C8 C8
C9 C9
C10 C10
C20 C20
H1 H1
H2C1 1H2C
H2C2 2H2C
H4 H4
H12 H12
H13 H13
H15 H15
H16 H16
H211 1H21
H212 2H21
H22 H22
H45 H45
H17 H17
H19 H19
H5 H5
H6 H6
H11 H11
H181 1H18
H182 2H18
H271 1H27
H272 2H27
H7 H7
H9 H9
H10 H10
H201 1H20
H202 2H20
H203 3H20