Atom Nomenclature for UQ1

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 UQ1

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C2 C2
O2 O2
CM2 CM2
C3 C3
O3 O3
CM3 CM3
C4 C4
O4 O4
C5 C5
CM5 CM5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
HM21 1HM2
HM22 2HM2
HM23 3HM2
HM31 1HM3
HM32 2HM3
HM33 3HM3
HM51 1HM5
HM52 2HM5
HM53 3HM5
H71 1H7
H72 2H7
H8 H8
H101 1H10
H102 2H10
H103 3H10
H111 1H11
H112 2H11
H113 3H11