Atom Nomenclature for SRE

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 SRE

Atom Name (V3) Atom Name (V2)
CL19 CL19
C16 C16
C15 C15
CL20 CL20
C17 C17
C18 C18
C13 C13
C14 C14
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C1 C1
N11 N11
C12 C12
C2 C2
C3 C3
H17 H17
H18 H18
H14 H14
H4 H4
H6 H6
H7 H7
H8 H8
H9 H9
H1 H1
H12 H12
H12A H12A
H2 H2
H2A H2A
H3 H3
H3A H3A
H16 H16
H171 H171