Atom Nomenclature for 898

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 898

Atom Name (V3) Atom Name (V2)
CL1 CL1
C1 C1
C2 C2
C3 C3
S2 S2
C4 C4
C5 C5
C6 C6
S1 S1
O2 O2
O1 O1
N1 N1
C12 C12
C13 C13
C14 C14
C50 C50
O3 O3
N2 N2
C15 C15
C21 C21
F1 F1
C22 C22
C26 C26
C27 C27
C24 C24
C28 C28
C8 C8
N3 N3
C9 C9
C7 C7
H2 H2
H3 H3
H51C H51C
H61C H61C
H1 H1
H12 H12
H131 H131
H132 H132
H141 H141
H142 H142
H22 H22
H24 H24
H26 H26
H28 H28
H81C H81C
H82C H82C
H83C H83C
H91C H91C
H92C H92C
H93C H93C
H71C H71C
H72C H72C
H73C H73C