Heme Binding Pocket of Myoglobin (Mb)

Clck here to view myoglobin's 8 alpha-helical segments (A-H) and their organization.

Unique Structural Properties of the Alpha-helix (PDF)

Explore the structure on the right by clicking on the labeled buttons or checkboxes to selectively modify portions of the structure shown.

Note the following features of this structure:

  • The iron (Fe) atom in the center of the heme protoporphyrin ring (green structure) is stabilized by the four nitrogren atoms of this ring, which make 4 metal coordination bonds with ferrous Fe II. These bonds thereby help prevent reduced Fe II from spontaneously oxidizing to the ferric Fe III state, which is nonfunction in terms of O2 transport because O2 does not bind reversibly to the ferric state.
  • The F helical segment depicted by the yellow ribbon (residues 58-76) includes amino acid sidechains that are in direct contact with the one side of the heme group, including the so-called proximal (F)-His 95 sidechain, which forms a 5th Fe (II) metal coordination bond with one of the imidazole ring basic nitrogen (N) atoms.
  • The E helical segment depicted by the lavendar ribbon (residues 58-76), with a subsegment highlight by an aqua ribbon (residues 57-71), includes amino acid sidechains that are in direct contact with other side of the heme group where O2 binds to Mb. Note that makes the 6th Fe II metal coordination on binding O2, which is further stabilizes in the complex by making an H-bond with one of the imidazole ring basic nitrogen (N) atoms of the so-called distal (E)-His 64 sidechain.
  • The H-bonds along the polypeptide backbones of α-helical segments E and F are represented by dashed lines between H-bonded atoms.
  • Even though the helices depicted in some of these images appear to "hollow" throughout the central axis, the spacefilled helical structures rendered with some of the checkboxes clearly show that no open space exists in the core of the α-helix because the polypeptide backbone atoms are packeted tightly together by virture of thier atom-specific van der Waal radii .


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© Duane W. Sears
April 13, 2021

Peptide Bond: Planar Structure
α-Helix: H-Bonding along the Polypeptide Backbone
Practice Quiz:  Secondary Structures
α-Helix: Right-Handed Staircase