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Myoglobin

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Crystal Structure of myoglobin, 1a6m
Crystal Structure of myoglobin, 1a6m
Sperm whale myoglobin complex with O2 and sulfate, 1a6m
Ligands: , ,
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml













Myoglobin is a globular protein whose function is to store molecular oxygen.

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 (for details see Oxymyoglobin). See also Molecular Playground/Myoglobin. 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)

Contents

3D Structures of Myoglobin

Update February 2013

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 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
1uvy – Mb – Paramecium caudatum
3qm5, 3qm6 – btMb – blackfin tuna

Mb 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, 1j52, 1lue, 1o16, 3ogb, 3obd, 3ock, 3sdn, 3o89, 4fwx, 4fwz - SwMb (mutant)
2bwh - SwMb (mutant) – Laue
3hc9, 3hen, 3heo, 3hep, 1nz2, 1nz3, 1rse, 1abs, 1xch, 1hrm, 1yma, 3rj6 - hoMb (mutant) – horse
2vlx , 2vly, 2vlz, 2vm0 – hoMb fragment
1dm1 – AlMb (mutant)
2mm1, 3rgk – hMb (mutant) – human

Mb containing a non-Fe protoporphyrin

1yog, 1yoh, 1yoi, 1myz – SwMb+Co protoporphyrin
3mn0 – SwMb (mutant)+Cu protoporphyrin+cyanide
1j3f – SwMb+Cr salophen
1ufj, 1ufp – SwMb (mutant)+Fe salophen
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
3rjn - hoMb+Zn deuteroporphyrin

Mb+NO

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

Mb+NO2

2frf, 2fri, 3lr7, 3lr9, 3vau, 3v2v, 3v2z - hoMb+NO2

Mb+O2

1ltw - SwMb (mutant)+O2
1a6m, 1mbo, 2z6s, 2z6t – SwMb+O2
1mno - pMb (mutant)+O2
3vm9 - hoMb + O

Mb+CO

2bw9, 1mz0 - SwMb (mutant)+CO – Laue
2g0r, 2g0s, 2g0v, 2g0x, 2g0z, 2g10, 2g11, 2g12, 2g14, 2blj, 1dxc, 1dxd, 1do1, 1do3, 1do4, 1do7, 1abs, 1mcy, 1mbc, 3nml – 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
3qm7 – btMb + CO

Mb+OH

1n9f – SwMb (mutant)+OH
1gjn – hoMb+OH

Mb+cyano compounds

2jho – SwMb cyanoMet
3qm8 - btMb cyanoMet
1ebc, 2cmm - SwMb+cyanide
1iop – SwMb+cyanide+hemin
108m, 101m, 104m, 105m, 2myc, 2myd, 2mya, 2mye, 2myb – SwMb+isocyanides
103m, 107m, 111m, 106m, 109m, 110m, 112m – SwMb (mutant) +isocyanides
3ba2 – hoMb+cyanide
2fal – AlMb+cyanide
2fam – AlMb+thiocyanate
1lht – stMb+cyanide
1emy – Mb+cyanide – asian elephant

Mb + N3

3qm9 – btMb + N3

MMb

1mgn, 1duk - SwMMb
1duo – SwMMb+methyl-imidazole
1myg, 1myh, 1myi, 1myj, 1ymb – pMMb
1myt – MMb – yellowfin tuna

Other complexes of Mb

3a2g – SwMb (mutant)+fluorescein
2w6x, 2w6y - SwMb (mutant)+Xe
2w6w - SwMb +Xe
2eb8, 2eb9 – SwMb+Cu
4fwy - SwMb (mutant)+ Cu
3ase – SwMb + RuO3
2ekt, 2eku – SwMb+methyl-depropionatehemin
2d6c – SwMb+porphycene
1swm, 1mbi – SwMb+imidazole
3u3e – SwMb + phenol
4h07 - SwMb (mutant)+ phenol
4h0b - SwMb (mutant)+ DMSO
1wvp – SwMb+tetrazolyl histidine
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
3qma - btMb+imidazole

apo-Mb

1bvc, 1bvd – SwApo-Mb + biliverdin

External Resources

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