Atom Nomenclature for 70U

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 70U

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
S2 S2
N3 N3
C4 C4
O4 O4
C5 C5
C6 C6
C5M C5M
C8 C8
O8 O8
O9 O9
C9 C9
C1' C1*
O2' O2*
C2' C2*
O3' O3*
C3' C3*
C4' C4*
O4' O4*
C5' C5*
O5' O5*
P P
OP1 O1P
OP2 O2P
OP3 O3P
HN3 HN3
H6 H6
H71 1H5M
H72 2H5M
H91 1H9
H92 2H9
H93 3H9
H1' H1*
HO2' 2HO*
H2' H2*
HO3' H3T
H3' H3*
H4' H4*
H5' 1H5*
H5'' 2H5*
HOP2 2HOP
HOP3 3HOP