Atom Nomenclature for LII

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 LII

Atom Name (V3) Atom Name (V2)
C4A C4A
C4 C4
C2 C2
C8A C8A
C5 C5
C6 C6
C7 C7
C5A C5A
C9 C9
C1' C1'
C2' C2'
C3' C3'
C4' C4'
C5' C5'
C6' C6'
C10 C10
C2X C2A'
C5X C5A'
N3 N3
N1 N1
N8 N8
N4 N4
N16 N16
O2' O2'
O5' O5'
H71 1H7
H51 1H5
H52 2H5
H53 3H5
H91 1H9
H3'1 1H3'
H4'1 1H4'
H6'1 1H6'
H101 1H10
H2A1 1H2A
H2A2 2H2A
H2A3 3H2A
H5'1 1H5'
H5'2 2H5'
H5'3 3H5'
H41 1H4
H42 2H4
H161 1H16
H162 2H16