Atom Nomenclature for D73

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 D73

Atom Name (V3) Atom Name (V2)
P P
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
N5 N5
C6 C6
C7 C7
C8 C8
C9 C9
PA PA
C1' C1'
C10 C10
N10 N10
N1A N1A
O1A O1A
C1B C1B
O1P O1P
C2' C2'
O2' O2'
C2A C2A
O2A O2A
C2B C2B
O2B O2B
O2P O2P
C3' C3'
O3' O3'
N3A N3A
C3B C3B
O3B O3B
O3P O3P
C4' C4'
O4' O4'
C4A C4A
C4B C4B
O4B O4B
C4X C4X
C5' C5'
O5' O5'
C5A C5A
C5B C5B
O5B O5B
C5X C5X
C6A C6A
N6A N6A
N7A N7A
C7M C7M
C8A C8A
C8M C8M
C9A C9A
N9A N9A
NAA NAA
CAB CAB
CAD CAD
CAE CAE
CAH CAH
CAI CAI
CAL CAL
CAM CAM
CAN CAN
CAO CAO
CAP CAP
HN3 HN3
HN5 HN5
H6 H6
H9 H9
H1' H1'
H1'A H1'A
HO1A HO1A
H1B H1B
HO1P HO1P
H2' H2'
HO2' HO2'
H2A H2A
H2B H2B
HO2B HO2B
H3' H3'
HO3' HO3'
H3B H3B
HO3B HO3B
H4' H4'
HO4' HO4'
H4B H4B
H5' H5'
H5'A H5'A
H5B H5B
H5BA H5BA
HN6A HN6A
HN6B HN6B
H7M H7M
H7MA H7MA
H7MB H7MB
H8A H8A
H8M H8M
H8MA H8MA
H8MB H8MB
HNAA HNAA
HAB HAB
HAD HAD
HAE HAE
HAH HAH
HAI HAI
HAL HAL
HALA HALA
HAM HAM
HAN HAN
HANA HANA
HANB HANB