Atom Nomenclature for AGG

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 AGG

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
S1 S1
O1 O1
O2 O2
N N
CA CA
CB CB
CG CG
CD1 CD1
CE1 CE1
CZ CZ
OH OH
CE2 CE2
CD2 CD2
C C
O O
OXT OXT
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
N18 N18
C18 C18
C19 C19
H11 1H1
H12 2H1
H13 3H1
H21 1H2
H22 2H2
H31 1H3
H32 2H3
H41 1H4
H42 2H4
H H
HA HA
HB1 1HB
HB2 2HB
HD1 HD1
HE1 HE1
HE2 HE2
HD2 HD2
HXT HXT
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H141 1H14
H142 2H14
H15 H15
H161 1H16
H162 2H16
H171 1H17
H172 2H17
H18 H18
H181 1H18
H182 2H18
H191 1H19
H192 2H19