Atom Nomenclature for XPB

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 XPB

Atom Name (V3) Atom Name (V2)
C4 C4
C5 C5
C6 C6
N1 N1
C8 C8
N2 N2
C10 C10
O6 O6
C11 C11
C12 C12
N3 N3
C13 C13
C14 C14
C15 C15
P P
OP1 OP1
OP2 OP2
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
C1' C1'
N9 N9
N7 N7
C2 C2
C16 C16
C17 C17
N1' N1'
C18 C18
O13 O13
H8 H8
H22 H22
H21 H21
H10 H10
H7 H7
H11 H11
H9 H9
H12 H12
H13 H13
H15 H15
H2 H2
H5' H5'
H5'' H5''
H4' H4'
H3' H3'
H3 H3
H2'' H2''
H2' H2'
H1' H1'
H16 H16
H17 H17
H18 H18
OP3 OP3
H1 H1