Atom Nomenclature for NXC

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 NXC

Atom Name (V3) Atom Name (V2)
CL CL
PT PT
C1 C1
C6 C6
C10 C10
N2 N2
C12 C12
C11 C11
C5 C5
C4 C4
C3 C3
C2 C2
C7 C7
N1 N1
C9 C9
C8 C8
C13 C13
C14 C14
C15 C15
P P
O2 O2
O1 O1
C16 C16
C17 C17
H10 H10
H10A H10A
H12 H12
H12A H12A
H12B H12B
H11 H11
H11A H11A
H11B H11B
H5 H5
H3 H3
H7 H7
H7A H7A
H9 H9
H9A H9A
H9B H9B
H8 H8
H8A H8A
H8B H8B
H13 H13
H13A H13A
H14 H14
H14A H14A
H15 H15
H15A H15A
H16 H16
H16A H16A
H17 H17
H17A H17A
H17B H17B
O3 O3
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
N3 N3
O4 O4
O5 O5
H30 H30
H31 H31
H32 H32
H33 H33