Atom Nomenclature for NR2

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 NR2

Atom Name (V3) Atom Name (V2)
S1 S1
N24 N24
O23 O23
O22 O22
C2 C2
C7 C7
C6 C6
C5 C5
N8 N8
C9 C9
O13 O13
N10 N10
S11 S11
O15 O15
O14 O14
C12 C12
C20 C20
C19 C19
C18 C18
C21 C21
C17 C17
C16 C16
C4 C4
C3 C3
H241 1H24
H242 2H24
H7 H7
H6 H6
HN8 HN8
H10 H10
H20 H20
H19 H19
H211 1H21
H212 2H21
H213 3H21
H17 H17
H16 H16
H4 H4
H3 H3