Atom Nomenclature for USM

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 USM

Atom Name (V3) Atom Name (V2)
OP2 OP2
P P
OP1 OP1
OP3 OP3
O5' O5'
N1 N1
C6 C6
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
C2' C2'
S2' S2'
C2A C2A
C5' C5'
C4' C4'
O4' O4'
C1' C1'
C3' C3'
O3' O3'
HOP2 HOP2
HOP3 HOP3
H6 H6
H5 H5
H2' H2'
H2A H2A
H2AA H2AA
H2AB H2AB
H5' H5'
H5'A H5'A
H4' H4'
H1' H1'
H3' H3'
HO3' HO3'
HN3 HN3