Atom Nomenclature for ORX

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 ORX

Atom Name (V3) Atom Name (V2)
OA OA
CA CA
OXT OXT
CAA CAA
NA NA
C4A C4A
C4 C4
C5 C5
C6 C6
N1 N1
C2 C2
C3 C3
O3 O3
C2A C2A
C5A C5A
OP4 OP4
P P
OP1 OP1
OP2 OP2
OP3 OP3
CBA CBA
CGA CGA
CDA CDA
NE NE
HOA HOA
HAA HAA
HNA HNA
H4A1 1H4A
H4A2 2H4A
H6 H6
HO3 HO3
H2A1 1H2A
H2A2 2H2A
H2A3 3H2A
H5A1 1H5A
H5A2 2H5A
HP2 HP2
HP3 HP3
HBA1 1HBA
HBA2 2HBA
HGA1 1HGA
HGA2 2HGA
HDA1 1HDA
HDA2 2HDA
HNE1 1HNE
HNE2 2HNE