Atom Nomenclature for UMS

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 UMS

Atom Name (V3) Atom Name (V2)
OP3 O3P
P P
OP1 O1P
OP2 O2P
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
SE2' SE2'
C1' C1'
CA' CA'
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
C6 C6
HOP3 HOP3
HOP2 HOP2
H5' H5'
H5'2 H5'2
H4' H4'
H3' H3'
HO3' H3T
H2' H2'
H1' H1'
HA' HA'
HA'2 HA'2
HA'3 HA'3
H3 H3
H5 H5
H6 H6