Atom Nomenclature for BLG

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 BLG

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
O5 O5
O1 O1
N2 N2
C7 C7
O7 O7
C8 C8
O3 O3
O4 O4
S4 S4
O41 O41
O42 O42
O43 O43
C6 C6
O6 O6
CA CA
CB CB
CG CG
CD CD
N N
C9 C9
O9 O9
C10 C10
O10 O10
N3 N3
C11 C11
C12 C12
S S
OS1 OS1
OS2 OS2
OS3 OS3
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
HN2 HN2
H81 1H8
H82 2H8
H83 3H8
HO3 HO3
HO43 3HO4
H61 1H6
H62 2H6
HO6 HO6
HA HA
HB HB
HG1 1HG
HG2 2HG
HD HD
HN1 1HN
HN2A 2HN
H91 1H9
H92 2H9
HO9 HO9
HN3 HN3
H111 1H11
H112 2H11
H121 1H12
H122 2H12
HOS3 3HOS