Atom Nomenclature for C38

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 C38

Atom Name (V3) Atom Name (V2)
O3P O3P
P P
O1P O1P
O2P O2P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
C1' C1*
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
N4 N4
C5 C5
C6 C6
I I
H3P H3P
H2P H2P
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
HA HA
H2'1 1H2*
H2'2 2H2*
H1' H1*
H4N1 1H4N
H4N2 2H4N
H6 H6