Atom Nomenclature for R47

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 R47

Atom Name (V3) Atom Name (V2)
O4 O4
N1 N1
O1 O1
C25 C25
C17 C17
C16 C16
C14 C14
C13 C13
C12 C12
C11 C11
C10 C10
C7 C7
C8 C8
C9 C9
C15 C15
CL1 CL1
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C18 C18
P1 P1
O2 O2
O3 O3
C19 C19
C20 C20
C21 C21
C22 C22
BR1 BR1
C23 C23
C24 C24
N2 N2
C26 C26
C30 C30
O7 O7
C27 C27
C28 C28
C29 C29
O5 O5
O6 O6
N3 N3
C31 C31
C35 C35
O10 O10
C32 C32
C33 C33
C34 C34
O8 O8
O9 O9
N4 N4
H10 H10
H8 H8
H9 H9
H7 H7
H17 H17
H18 H18
H5 H5
H6 H6
H1 H1
H2 H2
H3 H3
H4 H4
H12 H12
H11 H11
H31 H31
H13 H13
H14 H14
H15 H15
H16 H16
H24 H24
H19 H19
H20 H20
H21 H21
H23 H23
H22 H22
H32 H32
H25 H25
H26 H26
H27 H27
H28 H28
H30 H30
H29 H29
H33 H33
H34 H34
H35 H35