Atom Nomenclature for J1I

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 J1I

Atom Name (V3) Atom Name (V2)
N N1
C C1
O O1
P01 P1
C01 C2
N01 N2
O01 O2
OP3 O3
N02 N3
O02 O4
OP2 O5
C03 C3
N03 N4
O03 O6
OP1 O7
C04 C4
N04 N5
C05 C5
N05 N6
C06 C6
N06 N7
C07 C7
N07 N8
O07 O8
C08 C8
N08 N9
C09 C9
N09 N10
C10 C10
N10 N11
C11 C11
N11 N12
C12 C12
C13 C13
C14 C14
C15 C15
C17 C16
C18 C17
C19 C18
C20 C19
C21 C20
C22 C21
C23 C22
C24 C23
S S1
C02 C24
HN2 H1
HN3 H2
HC3 H3
HC1 H4
HC2 H5
H02 H6
H1 H7
H021 H8
H031 H10
H051 H12
H053 H13
H052 H14
H061 H15
H071 H17
H072 H18
H081 H19
H01 H20
H091 H21
H102 H22
H101 H23
H103 H24
H112 H25
H122 H28
H121 H29
H132 H30
H131 H31
H142 H32
H141 H33
H152 H34
H151 H35
H243 H37
H241 H38
H242 H39
HP2 H40
H111 H41