Atom Nomenclature for SCR

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 SCR

Atom Name (V3) Atom Name (V2)
C1 C1
O5 O5
C5 C5
C6 C6
O6 O6
S6 S6
O62 O62
O63 O63
O64 O64
C4 C4
O4 O4
S4 S4
O42 O42
O43 O43
O44 O44
C3 C3
O3 O3
S3 S3
O32 O32
O34 O34
O33 O33
C2 C2
O2 O2
S2 S2
O22 O22
O23 O23
O24 O24
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
O81 O81
O84 O84
O94 O94
O74 O74
O54 O54
O1 O1
O82 O82
O92 O92
O72 O72
O52 O52
O91 O91
O83 O83
O93 O93
O73 O73
O53 O53
O71 O71
O10 O10
O51 O51
S11 S11
S12 S12
S13 S13
S14 S14
H1 H1
H5 H5
H61 1H6
H62 2H6
H4 H4
H3 H3
H2 H2
H64 H64
H44 H44
H34 H34
H24 H24
H111 1H11
H112 2H11
H84 H84
H94 H94
H74 H74
H54 H54
H13 H13
H14 H14
H15 H15
H161 1H16
H162 2H16