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.
| Atom Name (V3) | Atom Name (V2) |
|---|---|
| P | P |
| OP1 | O1P |
| OP2 | O2P |
| O5' | O5' |
| C5' | C5' |
| C4' | C4' |
| O4' | O4' |
| C1' | C1' |
| N1 | N1 |
| C6 | C6 |
| C2 | C2 |
| O2 | O2 |
| N3 | N3 |
| C4 | C4 |
| O4 | O4 |
| C5 | C5 |
| C5A | C5A |
| C2' | C2' |
| O2' | O2' |
| CB' | CB' |
| CC' | CC' |
| OD' | OD' |
| CE' | CE' |
| CF' | CF' |
| NG' | NG' |
| CI' | CI' |
| CJ' | CJ' |
| C3' | C3' |
| O3' | O3' |
| HO2 | HO2 |
| H5'1 | H5'1 |
| H5'2 | H5'2 |
| H4' | H4' |
| H1' | H1' |
| HC6 | HC6 |
| HN3 | HN3 |
| H5A1 | H5A1 |
| H5A2 | H5A2 |
| H5A3 | H5A3 |
| H2' | H2' |
| HB'1 | HB'1 |
| HB'2 | HB'2 |
| HC'1 | HC'1 |
| HC'2 | HC'2 |
| HE'1 | HE'1 |
| HE'2 | HE'2 |
| HF'1 | HF'1 |
| HF'2 | HF'2 |
| HI'1 | HI'1 |
| HI'2 | HI'2 |
| HI'3 | HI'3 |
| HJ'1 | HJ'1 |
| HJ'2 | HJ'2 |
| HJ'3 | HJ'3 |
| H3' | H3' |
| HO3' | HO3' |
| OXT | OXT |
| HXT | H1 |