Atom Nomenclature for 16B

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 16B

Atom Name (V3) Atom Name (V2)
OP1 OAA
P PAE
OP3 OAD
OP2 OAF
O5' O5'
C5' C5'
C4' C4'
O4' O4'
C3' C3'
O3' O3'
C2' C2'
O2' O2'
C1' C1'
N1 NAM
C2 CAL
O2 OAK
N3 NAG
C6 CAN
C5 CAI
C4 CAH
N4 NAB
OAC OAC
HOP3 H1
HOP2 H2
H5' H3
H5'' H4
H4' H5
H3' H6
HO3' H7
H2' H8
HO2' H9
H1' H10
H6 H11
H5 H12
H41 H13
H14 H14