Atom Nomenclature for ON9

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 ON9

Atom Name (V3) Atom Name (V2)
C30 C1
C31 C2
C28 C3
C27 C4
C29 C5
C23 C6
C24 C7
C25 C8
C26 C9
C21 C10
C1 C11
O6 O1
O5 O2
C2 C12
C20 C13
C22 C14
C3 C15
O3 O3
C6 C16
O2 O4
C5 C17
C8 C18
C7 C19
C11 C20
C4 C21
O1 O5
C9 C22
C13 C23
C10 C24
C12 C25
C17 C26
O4 O6
C16 C27
C15 C28
C14 C29
C18 C30
C19 C31
O7 O7
C C32
N N1
O O8
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H30 H30
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35
H36 H36
H37 H37