Atom Nomenclature for FL9

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 FL9

Atom Name (V3) Atom Name (V2)
C2 C2
C3 C3
C3A C3A
C4 C4
C5 C5
C6 C6
C7 C7
C7A C7A
C21 C21
C1' C1*
C2' C2*
C3' C3*
C4' C4*
C5' C5*
C6' C6*
BR1 BR1
BR2 BR2
O1 O1
O3 O3
O4 O4
O6 O6
O2' O2*
O4' O4*
H5 H5
H7 H7
H21 H21
H6' H6*
HO4 HO4
HO6 HO6
HO2' *HO2
HO4' *HO4