Atom Nomenclature for E

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 E

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*
C1' C1*
N9 N9
C8 C8
N7 N7
C5 C5
C6 C6
N6 N6
N1 N1
C2 C2
N3 N3
C4 C4
C1 C1
C2A C2A
C3 C3
C3A C3A
C4A C4A
C5B C5B
C5M C5M
C6B C6B
C6A C6A
C7 C7
O7 O7
C8A C8A
O8 O8
C9 C9
O9 O9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
HOP2 2HOP
HOP3 3HOP
H5' 1H5*
H5'' 2H5*
H4' H4*
H3' H3*
HO3' *HO3
H2' 1H2*
H2'' 2H2*
H1' H1*
H8 H8
H6 H6
H2 H2
H1 H1
H2A H2A
H3 H3
H4A H4A
H5B H5B
H6B H6B
H7 H7
HO7 HO7
H8A H8A
HO8 HO8
H9 H9
HO9 HO9
H10 H10
H11 H11
H17 H17