Atom Nomenclature for XCF

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 XCF

Atom Name (V3) Atom Name (V2)
N4 N4
C3 C3
N5 N5
N2 N2
C1 C1
C8 C8
C6 C6
N7 N7
C9 C9
C10 C10
C11 C11
C27 C27
C28 C28
C14 C14
C24 C24
C25 C25
C26 C26
O13 O13
C12 C12
C15 C15
O16 O16
C17 C17
C18 C18
C21 C21
O19 O19
C20 C20
HN4 HN4
HN4A HN4A
H1 H1
HN7 HN7
HN7A HN7A
H9 H9
H9A H9A
H27 H27
H28 H28
H14 H14
H24 H24
H25 H25
H25A H25A
H26 H26
H26A H26A
H17 H17
H17A H17A
H17B H17B
H21 H21
H20 H20
H20A H20A
H20B H20B