Atom Nomenclature for AR9

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 AR9

Atom Name (V3) Atom Name (V2)
N1 N1
C3 C3
C5 C5
C8 C8
C10 C10
C13 C13
C16 C16
C19 C19
C22 C22
C25 C25
C28 C28
C31 C31
N32 N32
C34 C34
C36 C36
O37 O37
C38 C38
O42 O42
C43 C43
C47 C47
O49 O49
C51 C51
C54 C54
C56 C56
C60 C60
O61 O61
N62 N62
C64 C64
C67 C67
C70 C70
C73 C73
HN1 HN1
H3 H3
H5 H5
H5A H5A
H8 H8
H10 H10
H10A H10A
H13 H13
H13A H13A
H16 H16
H16A H16A
H19 H19
H19A H19A
H22 H22
H22A H22A
H25 H25
H25A H25A
H28 H28
H28A H28A
HN32 HN32
H34 H34
H38 H38
H38A H38A
H38B H38B
H43 H43
H43A H43A
H43B H43B
H47 H47
HO49 HO49
H51 H51
H51A H51A
H54 H54
H56 H56
H56A H56A
H56B H56B
HN62 HN62
H64 H64
H64A H64A
H67 H67
H67A H67A
H70 H70
H70A H70A
H73 H73
H73A H73A
H73B H73B