Atom Nomenclature for PN2

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 PN2

Atom Name (V3) Atom Name (V2)
CA CA
N N
C C
O O
CB CB
O5 O5
P6 P6
O7 O7
O8 O8
O9 O9
C11 C11
C12 C12
C13 C13
C14 C14
C10 C10
O10 O10
C9 C9
O39 O39
N8 N8
C7 C7
C42 C42
C43 C43
O44 O44
N4 N4
C3 C3
C47 C47
S1 S1
HN1 1HN
HN2 2HN
HCB1 1HCB
HCB2 2HCB
HOP6 6HOP
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H133 3H13
H141 1H14
H142 2H14
H143 3H14
H10 10H
H10O 10OH
HN8 8HN
H71 1H7
H72 2H7
H421 1H42
H422 2H42
HN4 4HN
H31 1H3
H2 2H
H471 1H47
H472 2H47
HS HS