Atom Nomenclature for RXR

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 RXR

Atom Name (V3) Atom Name (V2)
N1 N1
O1 O1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
SD SD
CE CE
C10 C10
S10 S10
H6 H6
H6A H6A
H6B H6B
H7 H7
H7A H7A
H7B H7B
H8 H8
H8A H8A
H8B H8B
H9 H9
H9A H9A
H9B H9B
HSD HSD
HE HE
HEA HEA
H10 H10
H10A H10A
HS10 HS10