Atom Nomenclature for RY7

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 RY7

Atom Name (V3) Atom Name (V2)
C1A C1A
C2A C2A
C3A C3A
C4A C4A
C5A C5A
C6A C6A
C7A C7A
O2A O2A
O3A O3A
O4A O4A
O6A O6A
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
N4 N4
O2 O2
O3 O3
O5 O5
O1 O1
H1A H1A
H2A H2A
H3A H3A
H4A H4A
H5A H5A
H6A1 H6A1
H6A2 H6A2
H7A1 H7A1
H7A2 H7A2
HOA2 HOA2
HOA3 HOA3
HOA4 HOA4
HOA6 HOA6
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H62 H62
H63 H63
H61 H61
HN41 HN41
HO2 HO2
HO3 HO3
HO1 HO1