Atom Nomenclature for PMJ

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 PMJ

Atom Name (V3) Atom Name (V2)
C7 C7
S8 S8
C4 C4
C5 C5
C6 C6
C1 C1
C2 C2
C3 C3
O10 O10
O9 O9
N11 N11
C12 C12
C30 C30
C31 C31
C32 C32
N33 N33
C34 C34
N35 N35
N37 N37
C13 C13
O14 O14
N15 N15
C16 C16
C17 C17
O18 O18
N19 N19
C20 C20
C21 C21
C26 C26
C25 C25
C24 C24
C27 C27
N28 N28
N29 N29
C23 C23
C22 C22
H7 H7
H7A H7A
H5 H5
H6 H6
H1 H1
H2 H2
H3 H3
HN11 HN11
H12 H12
H30 H30
H30A H30A
H31 H31
H31A H31A
H32 H32
H32A H32A
HN33 HN33
HN35 HN35
HN3A HN3A
HN37 HN37
HN15 HN15
H16 H16
H16A H16A
HN19 HN19
H20 H20
H20A H20A
H26 H26
H25 H25
HN28 HN28
HN29 HN29
HN2A HN2A
H23 H23
H22 H22