Atom Nomenclature for 39V

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 39V

Atom Name (V3) Atom Name (V2)
C59 C59
C58 C58
C57 C57
C56 C56
C55 C55
C54 C54
C53 C53
C52 C52
C51 C51
C50 C50
C2 C2
O3 O3
N1 N1
C11 C11
C12 C12
C13 C13
O14 O14
N15 N15
C16 C16
C26 C26
O27 O27
C17 C17
C66 C66
C65 C65
C67 C67
N69 N69
C68 C68
C63 C63
C60 C60
C62 C62
C61 C61
N28 N28
C29 C29
C31 C31
O32 O32
C37 C37
C38 C38
C39 C39
O40 O40
C30 C30
C41 C41
C42 C42
C43 C43
C44 C44
C45 C45
C46 C46
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H1 H1
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H2 H2
H3 H3
H24 H24
H34 H34
H19 H19
H23 H23
H20 H20
H22 H22
H25 H25
H26 H26
H37 H37
H38 H38
H39 H39
H40 H40
H41 H41
H42 H42
H27 H27
H28 H28
H33 H33
H32 H32
H31 H31
H30 H30
H29 H29
H36 H36