Atom Nomenclature for GRW

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 GRW

Atom Name (V3) Atom Name (V2)
C6 C1
C7 C2
C10 C3
C13 C4
C15 C5
C17 C6
C20 C7
C21 C8
C24 C9
C26 C10
C28 C11
C23 C12
N22 N1
C19 C13
C18 C14
C16 C15
C25 C16
S27 S1
O30 O1
O29 O2
N14 N2
O31 O3
C12 C17
C32 C18
C14 C19
O33 O4
N11 N3
O39 O5
C9 C20
C40 C21
C41 C22
C43 C23
C42 C24
N8 N4
O44 O6
N51 N5
N52 N6
N53 N7
C54 C25
C55 C26
C56 C27
C57 C28
C58 C29
C59 C30
C60 C31
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H30 H30
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35
H36 H36
H37 H37
H38 H38
H39 H39
H41 H41
H42 H42
H43 H43
H44 H44
H45 H45
H46 H46
H47 H47