Atom Nomenclature for 4XB

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 4XB

Atom Name (V3) Atom Name (V2)
C C
N N
O O
C1 C1
O1 O1
C2 C2
O2 O2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
OAQ OAQ
OAR OAR
H H
HA HA
HB HB
HN HN
H4 H4
H5 H5
H6 H6
H8 H8
H9 H9
H9A H9A
H10 H10
H10A H10A
H11 H11
H11A H11A
H12 H12
H12A H12A
H15 H15
H15A H15A
H15B H15B
H19 H19
H19A H19A
H21 H21
H22 H22
H23 H23
H25 H25