Atom Nomenclature for NDH

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 NDH

Atom Name (V3) Atom Name (V2)
OH2 OH2
C1 C1
C2 C2
OH1 OH1
C3 C3
C4 C4
C4A C4A
C8A C8A
C8 C8
C5 C5
C6 C6
C7 C7
HH2 HH2
H1 H1
H2 H2
HH1 HH1
H3 H3
H4 H4
H8 H8
H5 H5
H6 H6
H7 H7