Atom Nomenclature for C2E

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 C2E

Atom Name (V3) Atom Name (V2)
P1 P1
O2P O2P
O1P O1P
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
O6 O6
N1 N1
C2 C2
N2 N2
N3 N3
C4 C4
P11 P11
O21 O21
O11 O11
O5A O5A
C5A C5A
C4A C4A
O4A O4A
C3A C3A
O3A O3A
C2A C2A
O2A O2A
C1A C1A
N91 N91
C81 C81
N71 N71
C51 C51
C61 C61
O61 O61
N11 N11
C21 C21
N21 N21
N31 N31
C41 C41
HO2P HO2P
H5'1 H5'1
H5'2 H5'2
H4' H4'
H3' H3'
H2' H2'
HO2' HO2'
H1' H1'
H8 H8
HN1 HN1
HN21 HN21
HN22 HN22
HO21 HO21
H511 H511
H512 H512
H4A H4A
H3A H3A
H2A H2A
HO2A HO2A
H1A H1A
H81 H81
HN11 HN11
HN24 HN24
HN23 HN23