Atom Nomenclature for DW1

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 DW1

Atom Name (V3) Atom Name (V2)
O11 O11
C10 C10
RU RU
C12 C12
C13 C13
C14 C14
C16 C16
C17 C17
N20 N20
C6 C6
C5 C5
C4 C4
N18 N18
C22 C22
C27 C27
C26 C26
C25 C25
C24 C24
C23 C23
O15 O15
C28 C28
C21 C21
C7 C7
C3 C3
C29 C29
C2 C2
C30 C30
O8 O8
N19 N19
C1 C1
O9 O9
H12 H12
H13 H13
H14 H14
H16 H16
H17 H17
H6 H6
H5 H5
H4 H4
H26 H26
H24 H24
H23 H23
HO15 HO15
HN19 HN19