Atom Nomenclature for 1X4

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 1X4

Atom Name (V3) Atom Name (V2)
O1P O1P
P P
O2P O2P
O3P O3P
O5 O5'
C5 C5'
C4 C4'
O4 O1'
C3 C3'
C2 C2'
C1 C1'
O1 O1
H1A H1
H2A H2
H51 H3
H52 H4
H4 H5
H3 H6
H7 H7
H2 H8
H9 H9
H1 H10
HO1 H11