Atom Nomenclature for 4U3

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 4U3

Atom Name (V3) Atom Name (V2)
C2 C1
N3 N1
C4 C2
C5 C3
C6 C4
CL5 CL1
P P1
OP1 O1
OP2 O2
C5' C5
O5' O3
C4' C6
O4' O4
C3' C7
O3' O5
C2' C8
C1' C9
N1 N2
O2 O6
N4 N3
H6 H1
HOP2 H3
H5'' H4
H5' H5
H4' H6
H7 H7
HO3' H8
H2' H9
H2'' H10
H1' H11
H41 H12
H42 H13
OP3 O3P
HOP3 H2