Atom Nomenclature for JE2

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 JE2

Atom Name (V3) Atom Name (V2)
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C1 C1
C8 C8
C9 C9
O2 O2
O10 O10
C22 C22
N11 N11
O23 O23
C20 C20
C14 C14
C13 C13
C17 C17
C12 C12
O21 O21
C15 C15
C19 C19
C16 C16
C18 C18
C31 C31
N24 N24
O32 O32
C30 C30
C27 C27
C25 C25
C28 C28
C29 C29
S26 S26
N33 N33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
C39 C39
C40 C40
C41 C41
HC3 HC3
HC4 HC4
HC5 HC5
HC81 HC81
HC82 HC82
HC83 HC83
HO2 HO2
H11 H11
H20 H20
H131 H131
H132 H132
H17 H17
H12 H12
H21 H21
H15 H15
H19 H19
H16 H16
H18 H18
H30 H30
H251 H251
H252 H252
H281 H281
H282 H282
H283 H283
H291 H291
H292 H292
H293 H293
H33 H33
H341 H341
H342 H342
H37 H37
H38 H38
H39 H39
H40 H40
H411 H411
H412 H412
H413 H413