Atom Nomenclature for TC1

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 TC1

Atom Name (V3) Atom Name (V2)
P P
OP1 OP1
OP2 OP2
O5' O5*
C5' C5*
C4' C4*
C3' C3*
C2' C2*
C1' C1*
O4' O4*
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
C6 C6
C14 C14
C13 C13
N5 N5
C11 C11
S12 S12
C7 C7
C8 C8
C9 C9
C10 C10
O3' O3*
OP3 O3P
HP2 HP2
H5' 1H5*
H5'' 2H5*
H4' H4*
H3' H3*
H2' 1H2*
H2'' 2H2*
H1' H1*
H14 4H1
H5 5H
H7 7H
H8 8H
H9 9H
H10 0H1
HO3' H3T
HOP3 3HOP