Atom Nomenclature for N5I

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 N5I

Atom Name (V3) Atom Name (V2)
O3P O3P
OR2 OR2
NRO NRO
OR1 OR1
CZ3 CZ3
CE3 CE3
CD2 CD2
CH2 CH2
CZ2 CZ2
CE2 CE2
NE1 NE1
CD1 CD1
CG CG
C1' C1*
O4' O4*
C4' C4*
C3' C3*
O3' O3*
C2' C2*
C5' C5*
O5' O5*
P P
O2P O2P
O1P O1P
HOP3 3HOP
HE3 HE3
HH2 HH2
HZ2 HZ2
HD1 HD1
HG HG
H1' H1*
H4' H4*
H3' H3*
H3T H3T
H2'1 1H2*
H2'2 2H2*
H5'1 1H5*
H5'2 2H5*
HOP2 2HOP