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PDBsum entry 2e39
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Oxidoreductase
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PDB id
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2e39
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References listed in PDB file
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Key reference
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Title
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Structures of cyanide, Nitric oxide and hydroxylamine complexes of arthromyces ramosusperoxidase at 100 k refined to 1.3 a resolution: coordination geometries of the ligands to the haem iron.
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Authors
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K.Fukuyama,
T.Okada.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2007,
63,
472-477.
[DOI no: ]
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PubMed id
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Abstract
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1.3 A resolution crystal structures of the cyanide, nitric oxide and
hydroxylamine complexes of Arthromyces ramosus peroxidase (ARP), a class II
peroxidase belonging to the plant peroxidase superfamily, have been determined.
Anisotropic temperature factors were introduced for all non-H atoms of these
complexes using SHELX-97 and stereochemical constraints were applied to the
protein, protoporphyrin and sugar moieties, but not to the coordination
geometries to the haem iron. These refinements identified multiple conformations
for several side chains and revised the side-chain conformations of several
residues. Little difference was observed in the structures of the polypeptides,
haem and sugar moieties and in the coordinations to two calcium ions in these
complexes. Characteristic coordination geometries of each ligand to the haem
iron were observed. CN(-) binds to the haem iron in a tilt mode (Fe...C-N = 170
degrees ), whereas NO and hydroxylamine bind in bent modes (Fe...N-O = 125
degrees and Fe...NH(2)-OH = 111 degrees ). CN(-) is directed toward the distal
histidine (His56) and forms a hydrogen bond with the N(epsilon) atom, whereas NO
and hydroxylamine are directed away from His56. The Fe atoms of ARP-CN and
ARP-NO, in which the haem irons are both in low-spin states, are approximately
in the pyrrole N plane, whereas the iron in native ARP, which is in a
five-coordinated high-spin state, deviates markedly from the plane.
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Figure 1.
Figure 1 Schematic representation of ARP. The haem group is
shown in red and calcium ions in orange. The carbohydrates are
shown as stick models, in which C, N and O atoms are in yellow,
blue and red, respectively. This figure was prepared with the
program PyMOL (DeLano, 2002[DeLano, W. L. (2002). The PyMOL
Molecular Graphics System. DeLano Scientific LLC, San Carlos,
CA, USA.]).
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Figure 4.
Figure 4 Conformations of sugar moieties. (a) Two
N-acetylglucosamine residues bound to Asn143 and (b) mannose
residue bound to Ser339. The stick models are superimposed on
the (2F[o] - F[c]) map contoured at the 1.5  level.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2007,
63,
472-477)
copyright 2007.
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Secondary reference #1
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Title
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Crystal structure of the fungal peroxidase from arthromyces ramosus at 1.9 a resolution. Structural comparisons with the lignin and cytochrome c peroxidases.
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Authors
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N.Kunishima,
K.Fukuyama,
H.Matsubara,
H.Hatanaka,
Y.Shibano,
T.Amachi.
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Ref.
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J Mol Biol, 1994,
235,
331-344.
[DOI no: ]
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PubMed id
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Figure 8.
Figur 8. Superposition of ARP and LiP at the heme binding region. Yellow, ARP; blue, LiP.
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Figure 10.
Figure 10. Stereo views of the environments of 2 calcium sites. (a) Site 1; and (b) site 2. The interat~mic distances to
site 1 are: D570, 26 A; D570 a~, 25 G750, 26 A; 8790 y, 24 A; D77062, 2-6 ; Watt24, 2-5 A; and War425, 25 A.
Those to site 2 are: 81850, 2-5 A; S1850 y, 27 A; D202061, 25 A; D2020 a2, 2-6 A; T2040, 25 A; T20,10 yl, 27 A; V2070,
25 A; and D20906z, 26 A.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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