Atom Nomenclature for G2Y

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 G2Y

Atom Name (V3) Atom Name (V2)
C01 C1
C02 C2
C03 C3
C04 C4
C06 C5
C10 C6
C13 C7
C14 C8
C15 C9
C17 C10
C18 C11
C21 C12
O05 O1
O08 O2
O09 O3
O11 O4
O12 O5
O16 O6
O19 O7
O20 O8
CL1 CL1
CL2 CL2
CL3 CL3
H011 H1
H021 H2
H031 H3
H041 H4
H061 H5
H102 H6
H101 H7
H141 H8
H151 H9
H171 H10
H182 H11
H181 H12
H211 H13
H212 H14
H081 H15
H091 H16
H111 H17
H191 H18
H201 H19