Atom Nomenclature for 9SK

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 9SK

Atom Name (V3) Atom Name (V2)
C10 C1
C13 C2
C17 C3
C21 C4
C22 C5
C24 C6
C26 C7
C28 C8
C02 C9
C04 C10
C05 C11
C06 C12
C07 C13
C08 C14
C11 C15
C14 C16
C19 C17
C29 C18
C30 C19
C31 C20
C32 C21
C34 C22
C36 C23
C38 C24
C41 C25
C43 C26
C45 C27
C47 C28
C49 C29
C50 C30
F33 F1
F35 F2
F37 F3
F46 F4
F48 F5
N27 N1
N39 N2
N40 N3
O01 O1
O03 O2
O09 O3
O12 O4
O15 O5
O16 O6
O20 O7
O23 O8
O25 O9
O42 O10
O44 O11
S18 S1
H101 H1
H131 H2
H211 H4
H222 H5
H221 H6
H241 H7
H261 H8
H281 H9
H061 H10
H081 H11
H082 H12
H111 H13
H141 H14
H142 H15
H311 H17
H381 H18
H411 H19
H431 H20
H491 H21
H501 H22
H121 H23
H151 H24
H231 H25
H251 H26
H421 H27
H441 H28
H171 H29
H191 H30