Atom Nomenclature for UQ2

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 UQ2

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
CM2 CM2
CM3 CM3
CM5 CM5
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
O1 O1
O2 O2
O3 O3
O4 O4
H2M1 1H2M
H2M2 2H2M
H2M3 3H2M
H3M1 1H3M
H3M2 2H3M
H3M3 3H3M
H5M1 1H5M
H5M2 2H5M
H5M3 3H5M
H71 1H7
H72 2H7
H8 H8
H101 1H10
H102 2H10
H103 3H10
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H13 H13
H151 1H15
H152 2H15
H153 3H15
H161 1H16
H162 2H16
H163 3H16