Atom Nomenclature for INX

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 INX

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
O9 O9
N10 N10
C11 C11
C12 C12
N13 N13
O14 O14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
O20 O20
C21 C21
N22 N22
C23 C23
C24 C24
O25 O25
O26 O26
C27 C27
O28 O28
O29 O29
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
C39 C39
C40 C40
O41 O41
O42 O42
O43 O43
HC2 HC2
HC3 HC3
HC5 HC5
HC71 1HC7
HC72 2HC7
HC8 HC8
HN10 HN10
HN13 HN13
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H171 1H17
H172 2H17
H181 1H18
H182 2H18
H191 1H19
H192 2H19
H193 3H19
HC21 HC21
HN22 HN22
H231 1H23
H232 2H23
HO26 HO26
HO28 HO28
H301 1H30
H302 2H30
HC32 HC32
HC33 HC33
HC34 HC34
HC35 HC35
HC36 HC36
H381 1H38
H382 2H38
H391 1H39
H392 2H39
HO41 HO41