Atom Nomenclature for MKR

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 MKR

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
N2 N2
N12 N12
C8 C8
C14 C14
C15 C15
C18 C18
C20 C20
C9 C9
O25 O25
C26 C26
C27 C27
C28 C28
C29 C29
C30 C30
O1 O1
F1 F1
C7 C7
C10 C10
C11 C11
C12 C12
N3 N3
C16 C16
C17 C17
C19 C19
C21 C21
N1 N1
C22 C22
C24 C24
O2 O2
H2 H2
H5 H5
H6 H6
H15 H15
H91 1H9
H92 2H9
H93 3H9
H26 H26
H27 H27
H28 H28
H29 H29
H30 H30
H71 1H7
H72 2H7
H101 1H10
H102 2H10
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H161 1H16
H162 2H16
H171 1H17
H172 2H17
H191 1H19
H192 2H19
H211 1H21
H212 2H21
H241 1H24
H242 2H24
H243 3H24