Atom Nomenclature for X32

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 X32

Atom Name (V3) Atom Name (V2)
C3 C3
C2 C2
C1 C1
C6 C6
C5 C5
C4 C4
C7 C7
O8 O8
C9 C9
O22 O22
N10 N10
C11 C11
P12 P12
O24 O24
O23 O23
N13 N13
C14 C14
C15 C15
O29 O29
C25 C25
C26 C26
C27 C27
C28 C28
N16 N16
C17 C17
C18 C18
O37 O37
C30 C30
C31 C31
C36 C36
C32 C32
C35 C35
C33 C33
C34 C34
O19 O19
H3 H3
H2 H2
H1 H1
H6 H6
H5 H5
H7 H7
H7A H7A
HN10 HN10
H11 H11
H11A H11A
HO23 HO23
HN13 HN13
H14 H14
H25 H25
H25A H25A
H26 H26
H27 H27
H27A H27A
H27B H27B
H28 H28
H28A H28A
H28B H28B
HN16 HN16
H17 H17
H30 H30
H30A H30A
H36 H36
H32 H32
H35 H35
H33 H33
H34 H34
HO19 HO19