Atom Nomenclature for UN5

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 UN5

Atom Name (V3) Atom Name (V2)
O8 O8
C9 C9
N4 N4
C20 C20
C8 C8
N2 N2
C11 C11
C6 C6
C2 C2
C5 C5
N1 N1
S1 S1
O3 O3
O2 O2
O1 O1
C4 C4
C3 C3
C7 C7
C1 C1
C10 C10
O4 O4
C12 C12
C13 C13
C14 C14
C16 C16
C19 C19
C15 C15
C18 C18
C17 C17
N3 N3
S2 S2
O5 O5
O6 O6
O7 O7
HN4 HN4
H201 1H20
H202 2H20
H203 3H20
H8 H8
H111 1H11
H112 2H11
H2 H2
HN1 HN1
HO3 HO3
H4 H4
H71 1H7
H72 2H7
H1 H1
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H16 H16
H19 H19
H15 H15
H17 H17
HN3 HN3
HO5 HO5