Atom Nomenclature for U9K

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 U9K

Atom Name (V3) Atom Name (V2)
N1 N1
N2 N2
C3 C1
N4 N3
C6 C2
C7 C3
C9 C4
C10 C5
C11 C6
C12 C7
C13 C8
C14 C9
C15 C10
C16 C11
C18 C12
C19 C13
C20 C14
C1 C15
C2 C16
C4 C17
C5 C18
F1 F1
C8 C19
N3 N4
P1 P1
O1 O1
O2 O2
C17 C20
O3 O3
O4 O4
H5 H1
H24 H2
H25 H3
H26 H4
H6 H5
H8 H6
H9 H7
H10 H8
H12 H9
H13 H10
H15 H11
H14 H12
H17 H13
H16 H14
H19 H15
H18 H16
H23 H17
H22 H18
H28 H19
H27 H20
H1 H21
H2 H22
H3 H23
H4 H24
H7 H25
H11 H26
H29 H27
H21 H28
H20 H29
H30 H30