Atom Nomenclature for 9E2

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 9E2

Atom Name (V3) Atom Name (V2)
C11 C1
C5 C2
C9 C3
C8 C4
C7 C5
C6 C6
N4 N1
C2 C7
N1 N2
N3 N3
CL1 CL1
C3 C8
C4 C9
N5 N4
O5 O1
O4 O2
N2 N5
C1 C10
O1 O3
C12 C11
C10 C12
S1 S1
O3 O4
O2 O5
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12