Atom Nomenclature for RTY

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 RTY

Atom Name (V3) Atom Name (V2)
C C
N N
O O
C1 C1
O1 O1
C2 C2
C3 C3
C4 C4
C6 C6
CA CA
CB CB
CG CG
OH OH
CZ CZ
CD1 CD1
CD2 CD2
CE1 CE1
CE2 CE2
H5 H
H HN
H2 HNA
HO HO
H1 H1
H1A H1A
O2 O2
H3 H3
H3A H3A
H4 H4
H4A H4A
BR1 BR1
H6 H6
H6A H6A
HA HA
HB HB
HBA HBA
HD1 HD1
HD2 HD2
HE1 HE1
HE2 HE2
H20 H20