Atom Nomenclature for LYR

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 LYR

Atom Name (V3) Atom Name (V2)
N N
CA CA
C C
O O
OXT OXT
CB CB
CG CG
CD CD
CE CE
NZ NZ
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C80 C80
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
H H
H2 HN2
HA HA
HXT HXT
HB2 HB1
HB3 HB2
HG2 HG1
HG3 HG2
HD2 HD1
HD3 HD2
HE2 HE1
HE3 HE2
HZ HZ
H1 H1
H11 1H1
HC2 H2
H41 1H4
H42 2H4
H43 3H4
H5 H5
H6 H6
H7 H7
H81 1H8
H82 2H8
H83 3H8
H9 H9
H10 H10
H131 1H13
H132 2H13
H133 3H13
H141 1H14
H142 2H14
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H181 1H18
H182 2H18
H183 3H18
H191 1H19
H192 2H19
H193 3H19