Atom Nomenclature for SUR

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 SUR

Atom Name (V3) Atom Name (V2)
P P
OP1 O1P
OP2 O2P
OP3 O3P
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C3' C3'
C1' C1'
N1 N1
C2' C2'
C6 C6
C2 C2
C5 C5
S2 S2
N3 N3
C4 C4
O4 O4
O2' O2'
O3' O3'
HOP1 1HOP
HOP3 3HOP
H5'1 1H5'
H5'2 2H5'
H4' H4'
H3' H3'
H1' H1'
H2' H2'
HC6 HC6
HC5 HC5
HN3 HN3
HO2 HO2
HO3 HO3