Atom Nomenclature for RJA

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 RJA

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C2 C2
O2 O2
C3 C3
O3 O3
C4 C4
O4 O4
C5 C5
O5 O5
C6 C6
C7 C7
C8 C8
C9 C9
O1' O1'
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
HO1 HO1
H2 H2
H2A H2A
HO2 HO2
H3 H3
H3A H3A
HO3 HO3
H4 H4
H4A H4A
HO4 HO4
H5 H5
H6 H6
H7 H7
H9 H9
H10 H10
H11 H11
H11A H11A
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H18A H18A
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H24A H24A
H24B H24B
H25 H25
H25A H25A
H25B H25B
H26 H26
H26A H26A
H26B H26B
H27 H27
H27A H27A
H27B H27B
H28 H28
H28A H28A
H28B H28B