Atom Nomenclature for UN4

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 UN4

Atom Name (V3) Atom Name (V2)
C2 C2
C4 C4
C5 C5
C4' C4*
C3' C3*
C2' C2*
N9 N9
N3 N3
N2 N2
N1 N1
C6 C6
O6 O6
C60 C60
C14 C14
N7 N7
C8 C8
O14 O14
N15 N15
H4' H4*
H3'1 1H3*
H3'2 2H3*
H2'1 1H2*
H2'2 2H2*
H9 H9
H2N1 1H2N
H2N2 2H2N
H601 1H60
H602 2H60
H8 H8
H15 H15