Atom Nomenclature for 0PO

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 0PO

Atom Name (V3) Atom Name (V2)
C C10
O1 O1
N1 N1
C2 C1
C3 C2
C4 C3
C5 C4
C6 C5
C7 C6
C8 C7
C9 C8
C10 C9
N N2
CA C11
C1 C12
O O3
CB C13
CG1 C14
CG2 C15
N2 N3
CA1 C16
CC C17
OXT O5
CB1 C18
CG C19
CD1 C20
CD2 C21
CE1 C22
CE2 C23
CZ C24
CM C25
N11 N4
C21 C26
C31 C27
C41 C28
C51 C29
C61 C30
CD C31
O2 O6
N12 N6
C22 C36
C32 C37
C42 C38
C52 C39
C62 C40
CE C41
S S1
N3 N5
C1' C32
C2' C33
C3' C34
C4' C35
H3 H1
H4 H2
H5 H3
H6 H4
H7 H5
H8 H6
H H8
HA H10
HB H11
HG11 H12
HG12 H13
HG13 H14
HG21 H15
HG22 H16
HG23 H17
H1 H19
HA1 H21
HC H22
HOR H23
HB2 H24
HB3 H25
HD1 H26
HD2 H27
HE1 H28
HE2 H29
HZ H30
HM1 H31
HM2 H32
H2 H35
H31 H36
H32 H37
H41 H38
H51 H40
H52 H41
H61 H42
H62 H43
H21 H54
H42 H55
H53 H56
H63 H57
H11 H58
H2A H59
HN H44
H2'1 H45
H2'2 H46
H2'3 H47
H3'1 H48
H3'2 H49
H3'3 H50
H4'1 H51
H4'2 H52
H4'3 H53