Atom Nomenclature for KNI

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 KNI

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
N1 N1
O1 O1
O3 O3
N2 N2
C26 C26
C12 C12
S1 S1
C27 C27
C13 C13
O6 O6
C17 C17
N3 N3
O4 O4
C15 C15
C28 C28
C16 C16
C31 C31
C14 C14
O2 O2
C29 C29
C33 C33
C30 C30
C32 C32
N4 N4
C20 C20
C18 C18
C19 C19
S2 S2
C21 C21
O5 O5
N5 N5
C22 C22
C23 C23
C24 C24
C25 C25
H1 H1
H2 H2
H5 H5
H7 H7
H8 H8
H9 H9
H101 H101
H102 H102
HN2 HN2
H26 H26
H121 H121
H122 H122
H271 H271
H272 H272
H273 H273
HN3 HN3
H15 H15
H161 H161
H162 H162
H31 H31
H14 H14
HO2 HO2
H29 H29
H33 H33
H30 H30
H32 H32
H201 H201
H202 H202
H18 H18
H191 H191
H192 H192
HN5 HN5
H231 H231
H232 H232
H233 H233
H241 H241
H242 H242
H243 H243
H251 H251
H252 H252
H253 H253