Atom Nomenclature for T6A

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 T6A

Atom Name (V3) Atom Name (V2)
P P
OP1 O1P
OP2 O2P
OP3 O3P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
O2' O2*
C1' C1*
N9 N9
C8 C8
N7 N7
C5 C5
C6 C6
N6 N6
N1 N1
C2 C2
N3 N3
C4 C4
C10 C10
O10 O10
N11 N11
C12 C12
C13 C13
ODA O13A
ODB O13B
C14 C14
O14 O14
C15 C15
HOP2 2HOP
HOP3 3HOP
H5' 1H5*
H5'' 2H5*
H4' H4*
H3' H3*
HO3' H3T
H2' H2*
HO2' 2HO*
H1' H1*
H8 H8
HN6 HN6
H2 H2
HN1 HN1
H12 H12
H13 H13
H14 H14
HO4 HO4
H151 1H15
H152 2H15
H153 3H15