Atom Nomenclature for DUA

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 DUA

Atom Name (V3) Atom Name (V2)
N1 N1
O1 O1
C2 C2
N2 N2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
C6 C6
C1' C1'
C17 C17
C18 C18
C19 C19
C2' C2'
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
C3' C3'
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C4' C4'
O4' O4'
C5' C5'
HO1 HO1
HN2 HN2
H5 H5
H6 H6
H1' H1'
H19 H19
H2' H2'
H2'A H2'A
H20 H20
H21 H21
H22 H22
H23 H23
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H3' H3'
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35
H4' H4'
H5' H5'
H5'A H5'A
HN3 HN3