Atom Nomenclature for ADJ

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 ADJ

Atom Name (V3) Atom Name (V2)
PB PB
O1B O1B
O2B O2B
PA PA
O1A O1A
O2A O2A
O3A O3A
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C1' C1'
N9 N9
C4 C4
N3 N3
C2 C2
N1 N1
C6 C6
N6 N6
C5 C5
N7 N7
C8 C8
C2' C2'
O2' O2'
C3' C3'
O3' O3'
N1N N1N
C6N C6N
C5N C5N
C4N C4N
C3N C3N
C2N C2N
C7N C7N
O7N O7N
O5R O5R
C5R C5R
C4R C4R
O4R O4R
C1R C1R
C2R C2R
O2R O2R
C3R C3R
O3R O3R
P1 P1
O1P O1P
O2P O2P
O3P O3P
O5S O5S
C5S C5S
C4S C4S
O4S O4S
C1S C1S
N9X N9X
C4X C4X
N3X N3X
C2X C2X
N1X N1X
C6X C6X
N6X N6X
C5X C5X
N7X N7X
C8X C8X
C2S C2S
O2S O2S
C3S C3S
O3S O3S
HOB HOB
HOA HOA
H5'1 1H5'
H5'2 2H5'
H4' H4'
H1' H1'
H2 H2
HN61 1HN6
HN62 2HN6
H8 H8
H2' H2'
HO'2 2HO'
H3' H3'
HO'3 3HO'
H6N H6N
HC6N HC6N
H5N H5N
HC5N HC5N
H4N H4N
H2N H2N
HC2N HC2N
H7N H7N
HON7 7HON
H5R1 1H5R
H5R2 2H5R
H4R H4R
H1R H1R
H2R H2R
HOR2 2HOR
H3R H3R
HOR3 3HOR
HOP HOP
H5S1 1H5S
H5S2 2H5S
H4S H4S
H1S H1S
H2X H2X
HX61 1HX6
HX62 2HX6
H8X H8X
H2S H2S
HOS2 2HOS
H3S H3S
HOS3 3HOS