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PDBsum entry 1aiz
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Electron transport(cadmium binding)
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PDB id
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1aiz
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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 apo-Azurin from alcaligenes denitrificans at 1.8 a resolution.
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Authors
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W.E.Shepard,
R.L.Kingston,
B.F.Anderson,
E.N.Baker.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1993,
49,
331-343.
[DOI no: ]
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PubMed id
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Abstract
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The structure of apo-azurin from Alcaligenes denitrificans has been determined
at high resolution by X-ray crystallography. Two separate structure analyses
have been carried out, (i) on crystals obtained from solutions of apo-azurin and
(ii) on crystals obtained by removal of copper from previously formed crystals
of holo-azurin. Data to 1.8 A resolution were collected from the apo-azurin
crystals, by Weissenberg photography (with image plates) using synchrotron
radiation and by diffractometry, and the structure was refined by restrained
least-squares methods to a final R value of 0.160 for all data in the range
10.0-1.8 A. The final model of 1954 protein atoms, 246 water molecules (66
half-weighted), four SO(4)(2-) ions, and two low-occupancy (0.13 and 0.15) Cu
atoms has r.m.s. deviations of 0.012, 0.045 and 0.013 A from standard bond
lengths, angle distances and planar groups. For copper-removed azurin, data to
2.2 A were collected by diffractometry and the structure refined by restrained
least squares to a final R value of 0.158 for all data in the range 10.0-2.2 A.
The final model of 1954 protein atoms, 264 water molecules, two SO(4)(2-) ions,
two low occupancy (0.18 and 0.22) metal atoms and one unidentified atom
(modelled as S) has r.m.s. deviations of 0.013, 0.047 and 0.012 A from standard
bond lengths, angle distances and planar groups. The two structures are
essentially identical to each other and show no significant differences from the
oxidized and reduced holo-azurin structures. The ligand side chains move
slightly closer together following the removal of copper, with the radius of the
cavity between the three strongly binding ligands, His 46, His 117 and Cys 112,
shrinking from 1.31 A in reduced azurin to 1.24 A in oxidized azurin and 1.16 A
in apo-azurin. There is a suggestion of increased flexibility in one of the
copper-binding loops but the structure supports the view that the copper site
found in holo-azurin is a stable structure, defined by the constraints of the
polypeptide structure even in the absence of a bound metal ion.
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Figure 2.
Fig. 2. Electron density for the two sulfate ions bound o olecule
A o apo-azurin, taken from an omit map in which these ions
di not contribute to the phasing. (a) The sulfate ion, which is
also found in the oxidized and reduced holo-azurin structures,
bound to His 83N e2 and Gly 76NH. (b) The sulfate ion bound
betwen Lys 56 and Lys 122, with a thrd Lys side chain (from
Lys 38 of a neighbouring molecule) and a water olecule
completing the ite.
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Figure 9.
Fig. 9. Superposition of the copper binding sites of apo-azurin
(yellow), copper-removed aurin (green), oxidized azuin (blue)
and reduced azurin (purple). Th copper position in oxidized
azurin is shown with a cross.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1993,
49,
331-343)
copyright 1993.
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Added reference #1*
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Title
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Metal substitution in a blue-copper protein: the crystal structure of cadmium-azurin at 1.8 A resolution.
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Authors
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K.A.Blackwell,
B.F.Andersen,
E.N.Baker.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1994,
50,
263-270.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Copper site in the oxiized form of azurin frm Alcaligenes
denitrificans.
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Figure 5.
Fig. 5. Stereo diagram of the electron density (2Fo - Fc) at the metal site of Cd-azurin (shown for molecule B).
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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*Note, "added" references are those not in the PDB file but
which have either been obtained from the journal or suggested by the
author(s).
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Secondary reference #1
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Title
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Copper coordination geometry in azurin undergoes minimal change on reduction of copper(ii) to copper(i)
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Authors
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W.E.B.Shepard,
B.F.Anderson,
D.A.Lewandoski,
G.E.Norris,
E.N.Baker.
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Ref.
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j am chem soc, 1990,
112,
7817.
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Secondary reference #2
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Title
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Structure of azurin from alcaligenes denitrificans refinement at 1.8 a resolution and comparison of the two crystallographically independent molecules.
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Author
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E.N.Baker.
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Ref.
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J Mol Biol, 1988,
203,
1071-1095.
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PubMed id
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