Atom Nomenclature for 5CM

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 5CM

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
N3 N3
C4 C4
C5 C5
C5A C5A
C6 C6
O2 O2
N4 N4
C1' C1*
C2' C2*
C3' C3*
C4' C4*
O4' O4*
O3' O3*
C5' C5*
O5' O5*
P P
OP1 O1P
OP2 O2P
OP3 O3P
H5A1 1H5A
H5A2 2H5A
H5A3 3H5A
H6 H6
HN41 1HN4
HN42 2HN4
H1' H1*
H2' 1H2*
H2'' 2H2*
H3' H3*
H4' H4*
HO3' *HO3
H5' 1H5*
H5'' 2H5*
HOP2 2HOP
HOP3 3HOP