Atom Nomenclature for 6OP

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 6OP

Atom Name (V3) Atom Name (V2)
P P1
OP1 O1
OP2 O2
OP3 O3
C6' C1
C5' C2
C4' C3
O4' O4
C3' C4
O3' O5
C2' C5
O2' O6
C1' C6
CB' C7
CG' C8
OD' O7
CE' C9
N1 N1
C2 C10
O2 O8
N3 N2
C4 C11
O4 O9
C5 C12
C7 C13
C6 C14
H1 H1
HOP3 H2
H6' H3
H5' H5
H4' H7
H3' H8
HO3' H9
H2' H10
H1' H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H3 H19
H20 H20
H21 H21
H22 H22
H6 H23