Atom Nomenclature for T39

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 T39

Atom Name (V3) Atom Name (V2)
P P
OP1 OP1
OP2 OP2
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
O2' O2'
C1' C1'
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
C7 C7
C6 C6
CA' CA'
CD' CD'
CB' CB'
OC' OC'
OP3 OP3
HOP2 HOP2
H5' H5'
H5'' H5''
H4' H4'
H3' H3'
HO3' HO3'
H7 H7
H1' H1'
H3 H3
H71 H71
H72 H72
H73 H73
H6 H6
HCA2 HCA2
HCA1 HCA1
HCD1 HCD1
HCD2 HCD2
HCD3 HCD3
HCB1 HCB1
HCB2 HCB2
HOP3 HOP3