Atom Nomenclature for 9MR

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 9MR

Atom Name (V3) Atom Name (V2)
O2 O2B
C2 C2B
C3 C3B
O3 O3B
C4 C4B
O4 O4B
C5 C5B
C6 C6B
O6 O6B
O5 O5B
C1 C1B
O1 O3A
C3A C3A
C4A C4A
O4A O4A
C5M C5M
N5A N5A
C1A C1A
C2A C2A
C6A C6A
O6A O6A
HO2 HO2B
H2 H2B
H3 H3B
HO3 HO3B
H4 H4B
HO4 HO4B
H5 H5B
H61 H6B1
H62 H6B2
HO6 HO6B
H1 H1B
H3A H3A
H4A H4A
HO4A HO4A
H5M1 H5M1
H5M2 H5M2
HN5A HN5A
H1A1 H1A1
H1A2 H1A2
H2A H2A
H6A1 H6A1
H6A2 H6A2
HO6A HO6A