Atom Nomenclature for 439

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 439

Atom Name (V3) Atom Name (V2)
O3 O3
C25 C25
N2 N2
C8 C8
C7 C7
C9 C9
C10 C10
C11 C11
C6 C6
C5 C5
C4 C4
C3 C3
N1 N1
C2 C2
C1 C1
C14 C14
C13 C13
C12 C12
N3 N3
S1 S1
O1 O1
O2 O2
C15 C15
C24 C24
C23 C23
C18 C18
C17 C17
C16 C16
C22 C22
C21 C21
C20 C20
CL1 CL1
C19 C19
H14 H14
H121 H121
H122 H122
H7 H7
H9 H9
H10 H10
H3 H3
H51C H51C
H52C H52C
H41C H41C
H42C H42C
H21C H21C
H22C H22C
H23C H23C
H11C H11C
H12C H12C
H13C H13C
H131 H131
H132 H132
HA HA
H24 H24
H16 H16
H22 H22
H17 H17
H19 H19
H21 H21