Atom Nomenclature for DAU

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 DAU

Atom Name (V3) Atom Name (V2)
O6 O6
C6 C6
C5 C5
O5 O5
C4 C4
O4 O4
C3 C3
O3 O3
C2 C2
O2 O2
C1 C1
O1 O1
P2 P2
O3P O3P
O4P O4P
OPP OPP
P P
O1P O1P
O2P O2P
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
C1' C1'
N11 N11
C61 C61
C51 C51
C5A C5A
C21 C21
O21 O21
N31 N31
C41 C41
O41 O41
HO6 HO6
HC61 HC61
HC62 HC62
HC5 HC5
HC4 HC4
HO4 HO4
HC3 HC3
HO3 HO3
HC2 HC2
HO2 HO2
HC1 HC1
H4PO H4PO
H2PO H2PO
HC51 HC51
HC52 HC52
H4'C H4'C
H3'C H3'C
H3'O H3'O
HC21 HC21
HC22 HC22
H1'C H1'C
H61C H61C
H5A1 H5A1
H5A2 H5A2
H5A3 H5A3
H31N H31N