Atom Nomenclature for OEW

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 OEW

Atom Name (V3) Atom Name (V2)
O41 O1
C35 C1
N36 N1
C37 C2
C39 C3
C38 C4
C57 C5
O40 O2
C40 C6
C42 C7
C45 C8
C54 C9
C51 C10
N49 N2
C47 C11
O48 O3
N38 N3
C36 C12
O37 O4
C20 C13
C22 C14
C1 C15
C6 C16
C5 C17
C4 C18
C3 C19
C2 C20
N15 N4
C21 C21
O22 O5
C19 C22
C18 C23
C17 C24
C16 C25
N23 N5
C24 C26
O26 O6
O25 O7
C27 C27
C33 C28
C32 C29
C31 C30
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H30 H30
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35
H36 H36
H37 H37
H38 H38
H39 H39
H40 H40
H41 H41
H42 H42
H43 H43