Atom Nomenclature for N12

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 N12

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
N3 N3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
O13 O13
N14 N14
C15 C15
C16 C16
O17 O17
N18 N18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
N24 N24
C25 C25
O26 O26
O27 O27
C28 C28
N29 N29
N30 N30
C31 C31
C32 C32
C33 C33
C34 C34
H21A 1H2
H22A 2H2
HN3 HN3
H4 H4
H61 1H6
H62 2H6
H7 H7
H81 1H8
H82 2H8
H91 1H9
H92 2H9
H101 1H10
H102 2H10
H111 1H11
H112 2H11
H121 1H12
H122 2H12
HN14 HN14
HN18 HN18
H191 1H19
H192 2H19
H21 H21
H22 H22
H25 H25
HO27 HO27
HN29 HN29
H301 1H30
H302 2H30
H311 1H31
H312 2H31
H321 1H32
H322 2H32
H331 1H33
H332 2H33
H341 1H34
H342 2H34