Atom Nomenclature for KNA

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 KNA

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C2 C2
O2 O2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
HO1 HO1
H2 H2
H2A H2A
H3 H3
H3A H3A
H4 H4
H4A H4A
H5 H5
H5A H5A
H6 H6
H6A H6A
H7 H7
H7A H7A
H8 H8
H8A H8A
H9 H9
H9A H9A
H9B H9B