Atom Nomenclature for M24

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 M24

Atom Name (V3) Atom Name (V2)
P P
N1 N1
C2 C2
N3 N3
C4 C4
C5 C5
C6 C6
N6 N6
N7 N7
C8 C8
N9 N9
C1' C1*
O1P O1P
C2' C2*
O2' O2*
C24 C24
O25 O25
C26 C26
C27 C27
C28 C28
C29 C29
O2P O2P
C3' C3*
O3' O3*
C30 C30
C31 C31
C32 C32
N33 N33
O34 O34
C35 C35
N36 N36
C37 C37
C38 C38
C39 C39
O3P O3P
C4' C4*
O4' O4*
C40 C40
C41 C41
C42 C42
F43 F43
C5' C5*
O5' O5*
H2 H2
HN6 HN6
HN6A HN6A
H8 H8
H1' H1*
H2' H2*
HO2' HO2*
H27 H27
H28 H28
H29 H29
H3' H3*
HO3' HO3*
H31 H31
H38 H38
H39 H39
HO3P HO3P
H4' H4*
H40 H40
H41 H41
H5' H5*
H5'A H5*A