Atom Nomenclature for HE3

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 HE3

Atom Name (V3) Atom Name (V2)
C9 C9
C8 C8
O9 O9
C2 C2
N4' N4'
C4' C4'
N3' N3'
C2' C2'
CM2 CM2
N1' N1'
C6' C6'
C5' C5'
C7' C7'
N3 N3
C4 C4
CM4 CM4
C5 C5
C6 C6
C7 C7
O7 O7
PA PA
O2A O2A
O3A O3A
O1A O1A
PB PB
O1B O1B
O2B O2B
O3B O3B
S1 S1
H91 1H9
H92 2H9
H93 3H9
H8 H8
HO9 HO9
H4' H4'
HM21 1HM2
HM22 2HM2
HM23 3HM2
H6' H6'
H7'1 1H7'
H7'2 2H7'
HM41 1HM4
HM42 2HM4
HM43 3HM4
H61 1H6
H62 2H6
H71 1H7
H72 2H7
H2A H2A
H1B H1B
H2B H2B