Atom Nomenclature for 3SA

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 3SA

Atom Name (V3) Atom Name (V2)
C1X C1X
C2X C2X
C3X C3X
C4X C4X
C5X C5X
C6X C6X
O1X O1X
O2X O2X
O3X O3X
O4X O4X
O5X O5X
O6X O6X
C1Y C1Y
O2Y O2Y
C2Y C2Y
C4Z C4Z
C3Y C3Y
O3Y O3Y
C4Y C4Y
N4Y N4Y
C5Y C5Y
O5Y O5Y
C6Y C6Y
C1Z C1Z
C2Z C2Z
O2Z O2Z
C3Z C3Z
O3Z O3Z
O4Z O4Z
C5Z C5Z
C6Z C6Z
C7Z C7Z
O7Z O7Z
H1X H1X
H2X H2X
H3X H3X
H4X H4X
H5X H5X
H6X1 1H6X
H6X2 2H6X
H6 H6
H5 H5
H4 H4
H6X H6X
H1Y H1Y
H3 H3
H2Y H2Y
H4Z H4Z
H3Y H3Y
H2 H2
H1 H1
H4Y H4Y
H5Y H5Y
H6Y1 1H6Y
H6Y2 2H6Y
H6Y3 3H6Y
H1Z H1Z
H2Z H2Z
H7 H7
H3Z H3Z
H8 H8
H9 H9
H6Z H6Z
H7Z1 1H7Z
H7Z2 2H7Z
H7Z H7Z