Atom Nomenclature for 3AN

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 3AN

Atom Name (V3) Atom Name (V2)
PB PB
O1B O1B
O2B O2B
O3B O3B
PA PA
O1A O1A
O2A O2A
O3A O3A
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
N3' N3*
C2' C2*
O2' O2*
C1' C1*
N9 N9
C8 C8
N7 N7
C5 C5
C6 C6
N6 N6
N1 N1
C2 C2
N3 N3
C4 C4
HOB2 2HOB
HOB3 3HOB
HOA1 1HOA
H5'1 1H5*
H5'2 2H5*
HC'4 4HC*
HC'3 3HC*
H3'1 1H3*
H3'2 2H3*
HC'2 2HC*
HO'2 2HO*
HC'1 1HC*
HC8 8HC
HN61 1HN6
HN62 2HN6
HC2 2HC