Atom Nomenclature for 84T

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 84T

Atom Name (V3) Atom Name (V2)
O1P O1P
P P
O2P O2P
N N
C C
CA CA
CB CB
CG CG
CD2 CD2
CD1 CD1
OHB OHB
OH OH
O O
O5' O5'
C5' C5'
C4' C4'
C3' C3'
C2' C2'
O2' O2'
O4' O4'
C1' C1'
N9 N9
C4 C4
N3 N3
C2 C2
C8 C8
N7 N7
C5 C5
C6 C6
N1 N1
N6 N6
H1P H1P
H H
HA HA
HB HB
HH HH
HG HG
HHB HHB
HD21 HD21
HD22 HD22
HD23 HD23
HD11 HD11
HD12 HD12
HD13 HD13
H5'1 H5'1
H5'2 H5'2
H4' H4'
H3'1 H3'1
H3'2 H3'2
H2' H2'
HC HC
H8 H8
H2 H2
HN61 HN61
HN62 HN62
HC1' HC1'