Atom Nomenclature for P28

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 P28

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
O9 O9
O10 O10
N8 N8
C81 C81
C82 C82
O81 O81
O41 O41
C1' C1'
C2' C2'
C3' C3'
N3 N3
O31 O31
O32 O32
C4' C4'
O4' O4'
C5' C5'
N5 N5
O51 O51
O52 O52
C6' C6'
H2 H2
H3 H3
H5 H5
H6 H6
H71 1H7
H72 2H7
H8 H8
HO1 HO1
HN8 HN8
H821 1H82
H822 2H82
H823 3H82
H2' H2'
HO4 HO4
H6' H6'