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PDBsum entry 2dn3
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Oxygen storage/transport
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PDB id
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2dn3
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References listed in PDB file
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Key reference
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Title
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1.25 a resolution crystal structures of human haemoglobin in the oxy, Deoxy and carbonmonoxy forms.
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Authors
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S.Y.Park,
T.Yokoyama,
N.Shibayama,
Y.Shiro,
J.R.Tame.
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Ref.
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J Mol Biol, 2006,
360,
690-701.
[DOI no: ]
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PubMed id
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Abstract
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The most recent refinement of the crystallographic structure of oxyhaemoglobin
(oxyHb) was completed in 1983, and differences between this real-space refined
model and later R state models have been interpreted as evidence of
crystallisation artefacts, or numerous sub-states. We have refined models of
deoxy, oxy and carbonmonoxy Hb to 1.25 A resolution each, and compare them with
other Hb structures. It is shown that the older structures reflect the software
used in refinement, and many differences with newer structures are unlikely to
be physiologically relevant. The improved accuracy of our models clarifies the
disagreement between NMR and X-ray studies of oxyHb, the NMR experiments
suggesting a hydrogen bond to exist between the distal histidine and oxygen
ligand of both the alpha and beta-subunits. The high-resolution crystal
structure also reveals a hydrogen bond in both subunit types, but with subtly
different geometry which may explain the very different behaviour when this
residue is mutated to glycine in alpha or beta globin. We also propose a new set
of relatively fixed residues to act as a frame of reference; this set contains a
similar number of atoms to the well-known "BGH" frame yet shows a much
smaller rmsd value between R and T state models of HbA.
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Figure 1.
Figure 1. Stereo view of the final 2mF[o]–DF[c] electron
density map for oxyHbA, showing (a) the ligand at the α haem
and (b) the β chain. In the α subunit, a small peak of density
(roughly 1.5σ) is found about 2.2 Å from the oxygen
ligand and 3.1 Å from Leu29. Leu29 shows some sign of
adopting more than one rotamer, which may allow a partially
occupied water molecule into the haem pocket. Density is
contoured at 1.5σ. It can be seen that the O2 atom of the
ligand, not directly bonded to the haem, is better defined in
the α pocket than in the β haem pocket density. The lower
electron density in the β subunits is indicative of a weaker
bond to the distal histidine and greater rotation about the
Fe–O bond. Temperature factors for the O2 atoms are similar
(35 Å^2and 33 Å^2 in the α and β subunits,
respectively).
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Figure 2.
Figure 2. Stereo view of the final 2mF[o]–DF[c] electron
density map for COHb, showing (a) the α haem and (b) the β
haem. Density is contoured at 1.5σ. The C termini of the α and
β subunits are shown in (c) and (d), respectively. Tyr141α and
Tyr145β show substantial shifts compared to PDB 1HHO.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
360,
690-701)
copyright 2006.
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