Myoglobin

Myoglobin is a globular protein whose function is to store molecular oxygen. (KineMage currently not supported) View1 shows a ribbon diagram, in gray, of the "Globin" (protein) portion of sperm whale deoxymyoglobin in which its eight helical segments, A through H, are displayed with two strands. Use the "zoom" slider to properly size the molecule in the viewer. Toggle the "ANIMATE" button to sequentially color these helices and their preceding nonhelical segments in rainbow order. You can see that the globin consists mostly of alpha helices; it has no beta sheets and its nonhelical segments mostly serve as links that connect the helices. Look down the barrel of some of the longer helices. Are they all straight? The heme is shown, in pink, in wireframe form with its N, O, and Fe atoms displayed as blue, red, and orange balls. Note how the heme is almost completely enclosed by the globin. Which few chemical groups of the Heme are exposed to the solvent? (Clicking on atoms displays their identity in the lower left hand corner.) Can you rationalize this exposure? View1 is the standard view of Mb. Rotate the protein around to convince yourself that the globin is approximately disc-shaped with a diameter that is about twice its thickness. Turn on the "Main Chain" button to display the polypeptide backbone in white with its N and O atoms represented by blue and red balls. How closely does the ribbon follow the main chain? Click "Animate" until the Mb ribbon is gray. Turn off the "Mb Ribbon" button. What are the orientations of the main chain carbonyl groups and the amide N atoms relative to each other which allows formation of the H-bonds of the alpha helices (not drawn)? View2 is a closeup of the heme from the same direction as View1. Turn on the "HemeLigand" button to display, in cyan, the sidechain of His 93, the proximal His, liganding the heme's Fe(II) ion (white bond). The Fe(II) is also liganded in a square-planar array by the heme's four pyrrole N atoms and hence has a total of 5 pyramidally arranged ligands. In oxyMb, the reversibly bound O2 molecule ligands the Fe from the opposite side of the heme as does the proximal His so that the Fe(II) becomes octahedrally coordinated. The Fe atom is not oxidized by its O2 ligand; it remains in the Fe(II) oxidation state. Rotate the image about the vertical axis until you see heme edge-on. Is the Heme planar? Note that the Fe atom is displaced towards the proximal His by 0.55 Å from the best plane though the porphyrin ring atoms. In oxyMb, the Fe is only 0.22 Å out of the heme plane and still on the side of the proximal His.

Exercise in large part by John H. Connor (present address: Department of Microbiology, Boston University School of Medicine, 850 Harrison Ave, Boston, MA, 02118, USA)

To study the 3D structure of oxygenated myoglobin click here.

3D Structures of Myoglobin3D Structures of Myoglobin

Myoglobin (Mb) is an oxygen binding protein found in muscle tissue. It contains a heme group. Metmyoglobin (MMb) is the oxidized form of myoglobin.

Mb wild typeMb wild type

2zsn, 2zso, 2zsp, 2zsq, 2zsr, 2zss, 2zst, 2zsx, 2zsy, 2zsz, 2zt0, 2zt1, 2zt2, 2zt3, 2zt4, 3e4n, 3e55, 3e5i, 3e5o, 3ecl, 3ecx, 3ecz, 3ed9, 3eda, 3edb, 2z6s, 1u7r, 1u7s, 1jp6, 1jp8, 1jp9, 1jpb, 1jw8, 1f6h, 1bz6, 1bzp, 1a6k, 1a6n, 1vxa, 1vxb, 1vxc, 1vxd, 1vxe, 1vxf, 1vxg, 1vxh, 1mlq, 1moa, 1mob, 1moc, 1mod, 4mbn, 5mbn, 1mbn – SwMb - Sperm whale
1l2k, 1cq2, 1mbd – SwMb – Neutron
1wla, 1hsy, 2v1e, 2v1f, 2v1g, 2v1h, 2v1i, 2v1j, 2v1k – hoMb - horse
2nrl – BtMb – Blackfin tuna
1mba, 3mba, 4mba – AlMb - Aplysia limacine
1m6m, 1mwd, 1mnh, 1mnj, 1mnk, 1ycb, 1pmb – pMb - pig
1lhs – stMb – sea turtle
1mbs – Mb - seal

Mb mutants uncomplexedMb mutants uncomplexed

3m38, 3m39, 3m3a, 3m3b, 3k9z, 3h57, 3h58, 2e2y, 2ef2, 2oh8, 2oh9, 2oha, 2ohb, 2blh, 2bli, 1h1x, 1co8, 1n9h, 1n9i, 1n9x, 1naz, 1f63, 1f65, 1dti, 1co9, 1cp0, 1cp5, 1cpw, 1ch1, 1ch2, 1ch3, 1ch5, 1ch7, 1ch9, 1cik, 1cio, 1ofk, 1ofj, 102m, 1obm, 2mbw, 1tes, 1irc, 1mti, 1mtj, 1mtk, 1mlf, 1mlg, 1mlh, 1mlj, 1mlk, 1mll, 1mlm, 1mlo, 1mlr, 1mln, 1mls, 2mga, 2mgb, 2mgc, 2mgd, 2mge, 2mgf, 2mgg, 2mgh, 2mgi, 2mgj, 2mgk, 2mgl, 2mgm, 2spl, 2spm, 2spn, 2spo, 1fcs - SwMb (mutant)
2bwh - SwMb (mutant) – Laue
3hc9, 3hen, 3heo, 3hep, 1nz2, 1nz3, 1rse, 1abs, 1xch, 1hrm, 1yma - hoMb (mutant) – horse
2vlx , 2vly, 2vlz, 2vm0 – hoMb fragment
1dm1 – AlMb (mutant)
2mm1 – hMb (mutant) – human

Mb containing a non-Fe protoporphyrinMb containing a non-Fe protoporphyrin

1yog, 1yoh, 1yoi – SwMb+Co protoporphyrin 2o58, 2o5b – hoMb+Mn protoporphyrin 2o5l - hoMb+Mn protoporphyrin +methanol 2o5m - hoMb+Mn protoporphyrin +azide 2o5o, 2o5q - hoMb+Mn protoporphyrin +NO2 2o5s - hoMb+Co protoporphyrin +NO2 2o5t - hoMb+Co protoporphyrin

Mb+NOMb+NO

1jdo, 1mlu – SwMb+NO 1hjt – SwMb (mutant)+NO 2frj, 2frk - hoMb+NO 2nx0 – BtMb+NO

Mb+NO2Mb+NO2

2frf, 2fri - hoMb+NO2

Mb+O2Mb+O2

1ltw - SwMb (mutant)+O2 1a6m, 1mbo, 2z6s, 2z6t – SwMb+O2 1mno - pMb (mutant)+O2

Mb+COMb+CO

2bw9 - SwMb (mutant)+CO – Laue 2g0r, 2g0s, 2g0v, 2g0x, 2g0z, 2g10, 2g11, 2g12, 2g14, 2blj, 1dxc, 1dxd, 1do1, 1do3, 1do4, 1do7, 1abs,1mcy – SwMb (mutant)+CO 1bzr , 1a6g, 1ajg, 1ajh, 1spe, 1mym, 1mbc – SwMb+CO 1myf - SwMb+CO – NMR 2mb5 - SwMb+CO – Neutron 1dwr, 1dws, 1dwt – hoMb+CO 1mdn, 1m6c – pMb (mutant)+CO 1mwc, 1yca – pMb+CO

Mb+cyano compoundsMb+cyano compounds

2jho – SwMb cyanoMet 1ebc, 2cmm - SwMb+cyanide 1iop – SwMb+cyanide+hemin 108m, 101m, 104m, 105m, 2myc – SwMb+n-butyl-isocyanide 2myd - SwMb+n-propyl-isocyanide 2mya, 2mye - SwMb+n-ethyl-isocyanide 2myb - SwMb+n-methyl-isocyanide 103m, 107m, 111m – SwMb (mutant)+n-butyl-isocyanide 106m, 109m – SwMb (mutant)+n-ethyl-isocyanide 110m – SwMb (mutant)+n-methyl-isocyanide 112m - SwMb (mutant)+n-propyl-isocyanide 3ba2 – hoMb+cyanide 2fal – AlMb+cyanide 2fam – AlMb+thiocyanate 1lht – stMb+cyanide 1emy – Mb+cyanide – asian elephant

MMbMMb

1mgn - SwMMb 1myg, 1myh, 1myi, 1myj, 1ymb – pMMb 1myt – MMb – yellowfin tuna

Other complexes of MbOther complexes of Mb

3a2g – SwMb (mutant)+fluorescein 2w6x, 2w6y - SwMb (mutant)+Xe 2w6w - SwMb +Xe 2eb8, 2eb9 – SwMb+Cu 2ekt, 2eku – SwMb+methyl-depropionatehemin 2d6c – SwMb+porphycene 1swm, 1mbi – SwMb+imidazole 2evk – SwMb (mutant)+acetic acid 2evp - SwMb (mutant)+mercaptoethanol 1v9q - SwMb (mutant)+Mn salophen derivative 1dtm - SwMb (mutant)+4-methylimidazole 2nsr – hoMb+nitro methane 2nss - hoMb+nitro benzene 1azi - hoMb+azide 1bje – hoMb (mutant)+azide 1nz4 – hoMb (mutant)+Cd 1nz5 - hoMb (mutant)+Mn 2in4 - hoMb+Zn-DME 1gjn – hoMb+hydroxide 2nrm – BtMb S-nitrosylated 5mba – AlMb+azide 1mni – pMb+imidazole