Atom Nomenclature for PRT

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 PRT

Atom Name (V3) Atom Name (V2)
O1G O1
PG P1
O2G O2
O3G O3
O3B O4
PB P2
O1B O5
O2B O6
O3A O7
PA P3
O1A O8
O2A O9
O5' O10
C5' C1
C4' C2
O4' O11
C3' C3
O3' O12
C2' C4
O2' O13
C1' C5
N9 N1
C8 C6
C4 C7
C5 C8
N7 N2
C6 C9
N6 N3
N3 N4
C2 C10
N1 N5
C11 C11
C12 C12
O12 O14
C13 C13
O13 O15
O14 O16
C14 C14
C15 C15
O15 O17
P P4
O3P O18
O1P O19
O2P O20
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26