Atom Nomenclature for UCN

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 UCN

Atom Name (V3) Atom Name (V2)
O37 O37
C9 C9
N1 N1
C8 C8
O5 O5
C7 C7
C6 C6
C5 C5
C20 C20
C1 C1
C2 C2
C3 C3
C4 C4
N3 N3
C19 C19
C18 C18
N2 N2
C17 C17
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C11 C11
C10 C10
C21 C21
O4 O4
C25 C25
C24 C24
C23 C23
N4 N4
C28 C28
C22 C22
O6 O6
C27 C27
C26 C26
H37 H37
H9 H9
HN1 HN1
H1 H1
H2 H2
H3 H3
H4 H4
H13 H13
H14 H14
H15 H15
H16 H16
H25 H25
H241 1H24
H242 2H24
H23 H23
HN4 HN4
H281 1H28
H282 2H28
H283 3H28
H22 H22
H271 1H27
H272 2H27
H273 3H27
H261 1H26
H262 2H26
H263 3H26