Atom Nomenclature for 515

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 515

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
N4 N4
C9 C9
N1 N1
C10 C10
C11 C11
N2 N2
C12 C12
C13 C13
C14 C14
C15 C15
O1 O1
O4 O4
C23 C23
C8 C8
O8 O8
C7 C7
O5 O5
C24 C24
O6 O6
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
C30 C30
O9 O9
O10 O10
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
O11 O11
O12 O12
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
O2 O2
C41 C41
C42 C42
C43 C43
C44 C44
H31 1H3
H41 1H4
H91 1H9
H1 H1
H2 H2
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H141 1H14
H142 2H14
H151 1H15
H152 2H15
H231 1H23
H232 2H23
H233 3H23
H71 1H7
H72 2H7
H271 1H27
H281 1H28
H291 1H29
H301 1H30
H10 H10
H331 1H33
H361 1H36
H11 H11
H161 1H16
H171 1H17
H181 1H18
H191 1H19
H201 1H20
H202 2H20
H21 1H2
H411 1H41
H421 1H42
H431 1H43
H441 1H44