Atom Nomenclature for RUS

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 RUS

Atom Name (V3) Atom Name (V2)
P P
N1 N1
C2 C2
SE2 SE2
N3 N3
C4 C4
O4 O4
C5 C5
C6 C6
C1' C1*
O1P O1P
C2' C2*
O2' O2*
O2P O2P
C3' C3*
O3' O3*
O3P O3P
C4' C4*
O4' O4*
C5' C5*
O5' O5*
H5 H5
H6 H6
H1' H1*
H2' H2*
HO2' HO2*
HO2P HO2P
H3' H3*
HO3' HO3*
HO3P HO3P
H4' H4*
H5' H5*
H5'A H5*A
HSE2 HSE2