Atom Nomenclature for 2PP

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 2PP

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C1' C1'
C2' C2'
C3' C3'
O1 O1
O2 O2
H2 H2
H31 1H3
H32 2H3
H41 1H4
H42 2H4
H51 1H5
H52 2H5
H53 3H5
H1'1 1H1'
H1'2 2H1'
H2'1 1H2'
H2'2 2H2'
H3'1 1H3'
H3'2 2H3'
H3'3 3H3'
HO2 HO2