Atom Nomenclature for JMH

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 JMH

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C1
C5 C2
C1' C3
C2' C4
C3' C5
C4 C6
C4' C7
C5' C8
C6 C9
C31 C10
N3 N2
N4 N3
O2 O1
O2' O2
O3' O3
O4' O4
O5' O5
OP1 O6
OP2 O7
P P1
OP3 O8
H1 H1
H2 H2
H3 H3
H4 H4
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H16 H16
H17 H17
H18 H18
H19 H19