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PDBsum entry 1dwt
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Oxygen transport
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PDB id
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1dwt
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of a ligand-Binding intermediate in wild-Type carbonmonoxy myoglobin.
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Authors
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K.Chu,
J.Vojtchovský,
B.H.Mcmahon,
R.M.Sweet,
J.Berendzen,
I.Schlichting.
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Ref.
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Nature, 2000,
403,
921-923.
[DOI no: ]
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PubMed id
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Abstract
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Small molecules such as NO, O2, CO or H2 are important biological ligands that
bind to metalloproteins to function crucially in processes such as signal
transduction, respiration and catalysis. A key issue for understanding the
regulation of reaction mechanisms in these systems is whether ligands gain
access to the binding sites through specific channels and docking sites, or by
random diffusion through the protein matrix. A model system for studying this
issue is myoglobin, a simple haem protein. Myoglobin has been studied
extensively by spectroscopy, crystallography, computation and theory. It serves
as an aid to oxygen diffusion but also binds carbon monoxide, a byproduct of
endogenous haem catabolism. Molecular dynamics simulations, random mutagenesis
and flash photolysis studies indicate that ligand migration occurs through a
limited number of pathways involving docking sites. Here we report the 1.4 A
resolution crystal structure of a ligand-binding intermediate in carbonmonoxy
myoglobin that may have far-reaching implications for understanding the dynamics
of ligand binding and catalysis.
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Figure 1.
Figure 1: Position of the CO molecule in states A and B. a,
Electron-density map of F[obs](MbCO*) - F[obs](CO bound) shows
positive (black, 10  )
and negative (grey, 7 )
electron density at the position of CO* (B) and bound CO (A),
respectively. b, Electron density map of 2F[obs ]- F[calc] (1.0
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of state B generated by photolysis. The iron is located below
the haem plane; the CO molecule is shown almost along its axis.
c, Electron density map of 2F[obs ]- F[calc] (1.0 )
of state A. The iron is in the haem plane; CO is bound almost
perpendicular to the haem plane.
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Figure 2.
Figure 2: Position of the CO molecule in state D. a, Electron
density map of F[obs](Mb**CO) - F[obs ](CO rebound) shows
positive (black, 4.2 )
and negative (grey, 5.2 )
electron density below the haem and at the position of bound CO,
respectively. b, Electron density maps of 2F[obs ]-[]F[calc]
(1.0 ).
The iron is below the haem plane; no electron density associated
with CO is seen at the distal side of the haem, but a new peak
interpreted as CO* appears below the haem. c, The CO-bound
complex obtained after briefly thawing the photorelaxed complex
shown in a, b.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2000,
403,
921-923)
copyright 2000.
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Secondary reference #1
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Title
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A myoglobin variant with a polar substitution in a conserved hydrophobic cluster in the heme binding pocket.
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Authors
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R.Maurus,
C.M.Overall,
R.Bogumil,
Y.Luo,
A.G.Mauk,
M.Smith,
G.D.Brayer.
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Ref.
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Biochim Biophys Acta, 1997,
1341,
1.
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PubMed id
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Secondary reference #2
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Title
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Crystal structure of photolysed carbonmonoxy-Myoglobin.
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Authors
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I.Schlichting,
J.Berendzen,
G.N.Phillips,
R.M.Sweet.
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Ref.
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Nature, 1994,
371,
808-812.
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PubMed id
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Secondary reference #3
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Title
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Crystallization and preliminary diffraction data for horse heart metmyoglobin.
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Authors
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C.Sherwood,
A.G.Mauk,
G.D.Brayer.
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Ref.
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J Mol Biol, 1987,
193,
227.
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PubMed id
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