Atom Nomenclature for 1CC

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 1CC

Atom Name (V3) Atom Name (V2)
P P
OP1 OP1
OP2 OP2
O5' O5'
C5' C5'
C4' C4'
C3' C3'
C2' C2'
C1' C1'
O4' O4'
N1 N1
C6 C6
C5 C5
C4 C4
N4 N4
N3 N3
C2 C2
O2 O2
C21 C21
O22 O22
O23 O23
O3' O3'
HOP2 HOP2
H5'' H5''
H5' H5'
H4' H4'
H3' H3'
H2'' H2''
H2' H2'
H1' H1'
H6 H6
H42 H42
H41 H41
H5 H5
HO3' HO3'
OP3 OP3
HOP3 HOP3