Atom Nomenclature for JKA

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 JKA

Atom Name (V3) Atom Name (V2)
C10 C1
C13 C2
C01 C3
S02 S1
O03 O1
O04 O2
N05 N1
C06 C4
C07 C5
O08 O3
C09 C6
C11 C7
C12 C8
C14 C9
O15 O4
H101 H1
H102 H2
H131 H3
H132 H4
H011 H5
H012 H6
H013 H7
H062 H8
H061 H9
H071 H10
H081 H11
H091 H12
H111 H13
H122 H14
H121 H15
H141 H16
H151 H17