Atom Nomenclature for U0E

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 U0E

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
N1 N1
N2 N2
N3 N3
N4 N4
N5 N5
N6 N6
N7 N7
N8 N8
O1 O1
O2 O2
O3 O3
O4 O4
O5 O5
O6 O6
H11A 1H1
H12 2H1
H13A 3H1
H3 H3
H41 1H4
H42 2H4
H5 H5
H61 1H6
H62 2H6
H71 1H7
H72 2H7
H81 1H8
H82 2H8
H91 1H9
H92 2H9
H101 1H10
H102 2H10
H11 H11
H121 1H12
H122 2H12
H13 H13
H14 H14
H151 1H15
H152 2H15
H153 3H15
H161 1H16
H162 2H16
H163 3H16
H18 H18
H191 1H19
H192 2H19
H201 1H20
H202 2H20
H23 H23
H251 1H25
H252 2H25
H261 1H26
H262 2H26
H271 1H27
H272 2H27
HN1 HN1
HN2 HN2
HN31 1HN3
HN32 2HN3
HN4 HN4
HN51 1HN5
HN52 2HN5
HN6 HN6
HN7 HN7
HN81 1HN8
HN82 2HN8
HO2 HO2