Atom Nomenclature for EUS

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 EUS

Atom Name (V3) Atom Name (V2)
C6 C1
O1 O1
C11 C2
C12 C3
C13 C4
C21 C5
C22 C6
C23 C7
C31 C8
C32 C9
C33 C10
C41 C11
C42 C12
C43 C13
C51 C14
C52 C15
C53 C16
C61 C17
C62 C18
C83 C19
C93 C20
N12 N1
N21 N2
N32 N3
N33 N4
N61 N5
O11 O2
O2 O3
O23 O4
O43 O5
O51 O6
O52 O7
O53 O8
O62 O9
S S1
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
H33 H33
H34 H34
H36 H36
H38 H38
H39 H39
H41 H41
H42 H42
H43 H43