Atom Nomenclature for 4OC

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 4OC

Atom Name (V3) Atom Name (V2)
P P
OP1 O1P
OP2 O2P
O5' O5*
CM2 CM2
C5' C5*
C4' C4*
O4' O4*
C3' C3*
C2' C2*
O2' O2*
C1' C1*
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
N4 N4
C5 C5
C6 C6
CM4 CM4
O3' O3*
OP3 O3P
HM41 1HM4
HM42 2HM4
HM43 3HM4
HN4 HN4
H5 H5
H6 H6
H1' H1*
H4' H4*
H5' 1H5*
H5'' 2H5*
HOP3 3HOP
H3' H3*
HO3' H3T
H2' H2*
HM21 1HM2
HM22 2HM2
HM23 3HM2
HOP2 2HOP