Atom Nomenclature for 03R

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 03R

Atom Name (V3) Atom Name (V2)
C1 C1
N2 N2
C3 C3
O4 O4
C5 C5
C6 C6
F7 F7
C8 C8
C9 C9
O10 O10
N11 N11
C12 C12
C13 C13
F14 F14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
O25 O25
O26 O26
C27 C27
C28 C28
C29 C29
C30 C30
C31 C31
C32 C32
N33 N33
N34 N34
C35 C35
C36 C36
C37 C37
C38 C38
C39 C39
H11 H11
H13 H13
H16 H16
H17 H17
H19 H19
H20 H20
H21 H21
H221 1H22
H222 2H22
H231 1H23
H232 2H23
H233 3H23
H24 H24
H26 H26
H28 H28
H291 1H29
H292 2H29
H30 H30
H33 H33
H341 1H34
H342 2H34
H35 H35
H36 H36
H37 H37
H38 H38
H39 H39