Atom Nomenclature for US3

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 US3

Atom Name (V3) Atom Name (V2)
P P
N1 N1
C2 C2
SE2 SE2
N3 N3
C4 C4
O4 O4
C5 C5
C6 C6
C1' C1'
OP3 OP3
C2' C2'
OP2 OP2
C3' C3'
O3' O3'
C4' C4'
O4' O4'
C5' C5'
O5' O5'
C5A C5A
H6 H6
H1' H1'
HOP3 HOP3
H2' H2'
H2'A H2'A
HOP2 HOP2
H3' H3'
HO3' HO3'
H4' H4'
H5' H5'
H5'A H5'A
H5A H5A
H5AA H5AA
H5AB H5AB
HSE2 HSE2
OP1 OP1