Atom Nomenclature for X8U

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 X8U

Atom Name (V3) Atom Name (V2)
O2 O2
C20 C20
O1 O1
C19 C19
N4 N4
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C31 C31
C30 C30
C29 C29
C28 C28
C27 C27
S2 S2
C18 C18
C15 C15
C16 C16
C17 C17
C12 C12
C11 C11
C10 C10
C9 C9
C14 C14
C13 C13
C8 C8
N3 N3
N2 N2
C7 C7
S1 S1
C4 C4
C3 C3
C2 C2
N1 N1
C5 C5
C6 C6
C1 C1
H2 H2
H221 H221
H222 H222
H231 H231
H232 H232
H241 H241
H242 H242
H251 H251
H252 H252
H31 H31
H27 H27
H30 H30
H29 H29
H28 H28
H16 H16
H14 H14
H17 H17
H111 H111
H112 H112
H101 H101
H102 H102
H91C H91C
H92C H92C
HA HA
H3 H3
HB HB
H1 H1
H6 H6