Atom Nomenclature for A70

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 A70

Atom Name (V3) Atom Name (V2)
N1 N1
C C1
O O1
C2 C2
C3 C3
N4 N2
CM C4
C5 C5
C6 C6
C1 C7
C21 C8
N N3
C31 C9
C4 C10
O1 O2
C' C11
C1' C12
C2' C13
C3' C14
C4' C15
C5' C16
C6' C17
C11 C18
N2 N4
C7 C19
O2 O3
C22 C20
C32 C21
C41 C22
C51 C23
C12 C24
C23 C25
C33 C26
C1'1 C27
C2'1 C28
C3'1 C29
C4'1 C30
C5'1 C31
C6'1 C32
N21 N5
O11 O4
C13 C33
C24 C34
C8 C35
O3 O5
C1'2 C36
C2'2 C37
C3'2 C38
C14 C39
N3 N6
C25 C40
C34 C41
C42 C42
H21 H2
H22 H3
H31 H4
H32 H5
HM1 H6
HM2 H7
HM3 H8
H51 H9
H52 H10
H61 H11
H62 H12
H11 H13
H12 H14
H211 H15
H221 H16
H3 H19
H'1 H21
H'2 H22
H2' H23
H3' H24
H4' H25
H5' H26
H6' H27
H1 H28
H212 H32
H222 H33
H311 H34
H321 H35
H41 H36
H42 H37
H511 H38
H521 H39
H53 H40
H121 H42
H2 H43
H312 H44
H322 H45
H1' H46
H2'1 H47
H2'2 H48
H3'1 H49
H3'2 H50
H4'1 H51
H4'2 H52
H5'1 H53
H5'2 H54
H6'1 H55
H6'2 H56
HN22 H58
HO1 H59
H122 H61
H13 H62
H24 H63
H1'1 H65
H2'3 H66
H2'4 H67
H2'5 H68
H3'3 H69
H3'4 H70
H3'5 H71
H111 H72
H123 H73
HN21 H75
H213 H76
H223 H77
H313 H78
H323 H79
H411 H80
H421 H81
H43 H82