Atom Nomenclature for SU9

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 SU9

Atom Name (V3) Atom Name (V2)
N5' N5'
C4' C4'
N3' N3'
C2' C2'
C1' C1'
C6' C6'
C9 C9
C8 C8
O10 O10
N7 N7
C5 C5
C6 C6
C1 C1
C2 C2
O11 O11
C12 C12
C3 C3
C4 C4
H5' H5'
H4' H4'
H2' H2'
H6' H6'
HN7 HN7
H6 H6
H1 H1
H121 1H12
H122 2H12
H123 3H12
H3 H3