Atom Nomenclature for 1MM

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 1MM

Atom Name (V3) Atom Name (V2)
C4 C4
C5 C5
C6 C6
C1 C1
C2 C2
C3 C3
S7 S7
N8 N8
C9 C9
N10 N10
C2' C2'
N1' N1'
C6' C6'
N5' N5'
C4' C4'
N3' N3'
O7A O7A
O7B O7B
O9 O9
C11 C11
O12 O12
C13 C13
O11 O11
O4' O4'
C5' C5'
C7' C7'
H4 H4
H5 H5
H6 H6
H3 H3
HN8 HN8
H10 H10
H131 1H13
H132 2H13
H133 3H13
H5'1 1H5'
H5'2 2H5'
H5'3 3H5'
H7'1 1H7'
H7'2 2H7'
H7'3 3H7'