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PDBsum entry 1a4c
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Electron transport
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PDB id
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1a4c
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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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Rack-Induced metal binding vs. Flexibility: met121his azurin crystal structures at different ph.
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Authors
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A.Messerschmidt,
L.Prade,
S.J.Kroes,
J.Sanders-Loehr,
R.Huber,
G.W.Canters.
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Ref.
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Proc Natl Acad Sci U S A, 1998,
95,
3443-3448.
[DOI no: ]
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PubMed id
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Abstract
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The rack-induced bonding mechanism of metals to proteins is a useful concept for
explaining the generation of metal sites in electron transfer proteins, such as
the blue copper proteins, that are designed for rapid electron transfer. The
trigonal pyramidal structure imposed by the protein with three strong equatorial
ligands (one Cys and two His) provides a favorable geometry for both cuprous and
cupric oxidation states. However, the crystal structures of the Met121His mutant
of azurin from Alcaligenes denitrificans at pH 6.5 (1.89- and 1.91-A
resolutions) and pH 3.5 (2.45-A resolution) show that the preformed metal
binding cavity in the protein is more flexible than expected. At high pH (6.5),
the Cu site retains the same three equatorial ligands as in the wild-type azurin
and adds His121 as a fourth strong ligand, creating a tetrahedral copper site
geometry with a green color referred to as 1.5 type. In the low pH (3.5)
structure, the protonation of His121 causes a conformational change in residues
117-123, moving His121 away from the copper. The empty coordination site is
occupied by an oxygen atom of a nitrate molecule of the buffer solution. This
axial ligand is coordinated less strongly, generating a distorted tetrahedral
copper geometry with a blue color and spectroscopic properties of a type-1 site.
These crystal structures demonstrate that blue copper proteins are flexible
enough to permit a range of movement of the Cu atom along the axial direction of
the trigonal pyramid.
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Figure 1.
Fig. 1. Copper site of A. denitrificans Met121His azurin.
(A) High pH form. The indicated distances are the mean values
over the subunits in HP1 and HP2. (B) Low pH form. The displayed
distances are the mean values between subunits C and D of LP.
Image produced with SETOR (24).
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Figure 3.
Fig. 3. Overlay of the low pH form (subunit D of LP,
blue) onto high pH form (subunit A of LP, green) of the copper
sites and the polypeptide stretch 120-124. The included
2.45-Å resolution F[o]-F[c] omit electron density map was
calculated with residues 120-123, and nitrate in subunits D was
removed and running a 200-cycle positional refinement before map
calculation. The map has been contoured at 3.0  . Image
produced with SETOR (24).
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