Atom Nomenclature for A5A

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 A5A

Atom Name (V3) Atom Name (V2)
N N
CA CA
CB CB
C C
O O
N3S N3S
S S
O1S O1S
O2S O2S
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
O2' O2*
C1' C1*
N9 N9
C8 C8
N7 N7
C5 C5
C6 C6
N6 N6
N1 N1
C2 C2
N3 N3
C4 C4
H H
HN2 HN2
HA HA
HB1 1HB
HB2 2HB
HB3 3HB
H3S H3S
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
H3T H3T
H2' H2*
HO'2 2HO*
H1' H1*
H8 H8
H61 1H6
H62 2H6
H2 H2