Atom Nomenclature for V3L

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 V3L

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
N3 N3
C4 C4
C5 C5
C6 C6
N6 N6
N7 N7
C8 C8
N9 N9
P P
PB PB
C10 C1''
C1' C1'
OP3 OP3
O1B O1B
C12 C2''
O12 O2''
C2' C2'
O2' O2'
OP1 OP1
O2B O2B
C13 C3''
O13 O3''
C3' C3'
O3' O3'
OP2 OP2
O3B O3B
C14 C4''
O14 O4''
C4' C4'
O4' O4'
C15 C5''
O15 O5''
C5' C5'
O5' O5'
H2 H2
HN6 HN6
HN6A HN6A
H8 H8
H1'' H1''
H1' H1'
HOP3 HOP3
HO1B HO1B
H2'' H2''
HO2' HO2'
H2' H2'
H3'' H3''
HO13 HO3A
H3' H3'
HO3' HO3'
HOP2 HOP2
HO3B HO3B
H4'' H4''
H4' H4'
H5'' H5''
H5AA H5AA
H5' H5'
H5'A H5'A