Atom Nomenclature for A1R

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 A1R

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
N3 N3
C4 C4
C5 C5
C6 C6
N6 N6
N7 N7
C8 C8
N9 N9
C1' C1*
C2' C2*
O2' O2*
C3' C3*
O3' O3*
O4' O4*
C4' C4*
C5' C5*
O5' O5*
PA PA
O1A O1A
O2A O2A
O3A O3A
PB PB
O1B O1B
O2B O2B
O5N O5N
C5N C5N
N4N N4N
C1N C1N
O2N O2N
C2N C2N
O3N O3N
C3N C3N
C4N C4N
H2 H2
HN61 1HN6
HN62 2HN6
H8 H8
H1' H1*
H2' H2*
HO2' HO2*
H3' H3*
HO3' HO3*
H4' H4*
H5'1 1H5*
H5'2 2H5*
HO2A HO2A
HO1B HO1B
H5N1 1H5N
H5N2 2H5N
HN4N HN4N
H1N1 1H1N
H1N2 2H1N
HO2N HO2N
H2N H2N
HO3N HO3N
H3N H3N
H4N H4N