Atom Nomenclature for NIU

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 NIU

Atom Name (V3) Atom Name (V2)
CA CA
CA2 CA2
OA2 OA2
OA3 OA3
CA4 CA4
CA5 CA5
CA6 CA6
OA6 OA6
CB1 CB1
CB2 CB2
CB3 CB3
CB4 CB4
CB5 CB5
CB6 CB6
CG1 CG1
CG2 CG2
CG3 CG3
CD1 CD1
CD2 CD2
CD3 CD3
CD4 CD4
CD5 CD5
HO6 HO6
HB2 HB2
HB3 HB3
HB4 HB4
HB5 HB5
HB6 HB6
HG1 HG1
HG21 1HG2
HG22 2HG2
HG31 1HG3
HG32 2HG3
HG33 3HG3
HD11 1HD1
HD12 2HD1
HD21 1HD2
HD22 2HD2
HD31 1HD3
HD32 2HD3
HD41 1HD4
HD42 2HD4
HD51 1HD5
HD52 2HD5