Atom Nomenclature for J1A

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 J1A

Atom Name (V3) Atom Name (V2)
C1 C1
N1 N1
O1 O1
S1 S1
C2 C2
N2 N2
O2 O2
C3 C3
N3 N3
O3 O3
C4 C4
N4 N4
O4 O4
C5 C5
N5 N5
C6 C6
N6 N6
C7 C7
C8 C8
N8 N8
C9 C9
N9 N9
C10 C10
N10 N10
C11 C11
N11 N11
C12 C12
N12 N12
C13 C13
C14 C14
C15 C15
C16 C16
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C25 C25
C26 C26
C27 C27
N28 N28
H1 H1
H2 H2
HO2 HO2
H3 H3
HN3 HN3
HN3A HN3A
HO3 HO3
H4 H4
H5 H5
H8 H8
HN9 HN9
HN9A HN9A
H10 H10
H10A H10A
HN10 HN10
H11 H11
H12 H12
H12A H12A
H13 H13
H13A H13A
H14 H14
H14A H14A
H15 H15
H15A H15A
H16 H16
H16A H16A
H18 H18
H18A H18A
H22 H22
H27 H27
H27A H27A
HN28 HN28