Atom Nomenclature for 04J

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 04J

Atom Name (V3) Atom Name (V2)
C C
N N
O O
N1 N1
O1 O1
C2 C2
O2 O2
N3 N3
C4 C4
N5 N5
C6 C6
C7 C7
N8 N8
C9 C9
CA CA
CB CB
CD CD
CG CG
CT CT
N10 N10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C4A C4A
C8A C8A
NA2 NA2
NA4 NA4
OE1 OE1
OE2 OE2
HN HN
HO2 HO2
H7 H7
H9 H9
H9A H9A
HA HA
HB HB
HBA HBA
HG HG
HGA HGA
HN10 HN10
H12 H12
H13 H13
H15 H15
H16 H16
HNA2 HNA2
HNAA HNAA
HNA4 HNA4
HNAB HNAB
HOE2 HOE2