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PDBsum entry 1hsr
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Oxidoreductase
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PDB id
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1hsr
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References listed in PDB file
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Key reference
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Title
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Binding mode of benzhydroxamic acid to arthromyces ramosus peroxidase shown by x-Ray crystallographic analysis of the complex at 1.6 a resolution.
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Authors
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H.Itakura,
Y.Oda,
K.Fukuyama.
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Ref.
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Febs Lett, 1997,
412,
107-110.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of Arthromyces ramosus peroxidase (ARP) in complex with
benzhydroxamic acid (BHA) as determined by X-ray analysis at 1.6 A shows
unambiguously how BHA binds to ARP. BHA is located in the distal heme pocket.
Its functional groups are held by three hydrogen bonds to His56N(epsilon),
Arg52N(epsilon), and Pro(154)O, but are too far away to interact with the heme
iron. The aromatic ring of BHA is positioned at the entrance of the channel to
the heme pocket, approximately parallel to the heme group. Most water molecules
at the active site of the native enzyme are replaced by BHA, leaving a ligand,
probably a water molecule, at the sixth position of the heme. Results are
compared with spectroscopic data.
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Figure 1.
Fig. 1. The BHA and SHA structures with the atom numberings
used in the text.
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Figure 3.
Fig. 3. Environment of the BHA molecule shown by a
stereo-pair. Possible hydrogen bonds involving BHA are shown by
broken lines. The lower side of the figure is the surface of the
ARP molecule. The hydrogen bond distances for BHA are
O(7)…Arg^52N[ε], 3.3 Å; N(7)…Pro^154O, 2.8 Å;
O(8)…His^56N[ε], 2.6 Å; and O(8)…415, 2.7 Å.
The respective distances of Fe…415 and Fe…O(8) are 2.7
Å and 4.4 Å. The distance between C(1) in BHA and
the methyl carbon bonded to C(18) in the heme is 3.9 Å.
The torsion angle about C(1)−C(7) bond of BHA is 14°. The
dihedral angle between the benzene ring of BHA and the pyrrole D
ring of the heme is 9°.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
Febs Lett
(1997,
412,
107-110)
copyright 1997.
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Secondary reference #1
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Title
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Binding of iodide to arthromyces ramosus peroxidase investigated with x-Ray crystallographic analysis, 1h and 127i nmr spectroscopy, And steady-State kinetics.
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Authors
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K.Fukuyama,
K.Sato,
H.Itakura,
S.Takahashi,
T.Hosoya.
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Ref.
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J Biol Chem, 1997,
272,
5752-5756.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Electron densities of the (F[o]  F[c]) (A)
and anomalous difference (B) Fourier maps for the iodide
derivative superimposed on the C  model of^
ARP. The density for the (F[o] F[c]) map
is drawn at 6  and^ that
for anomalous difference map at 2.2 .
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Figure 2.
Fig. 2. Stereo view showing the iodide-binding site and its
environment on the heme distal side. The iodine and iron atoms
are shown by yellow and purple globes with their van der Waals
radii. Water molecules are shown by red globes with 40% of the^
oxygen atom's van der Waals radius. The peptide of
Phe^90-Pro91-Ala^92 is in orange and that of
Ser151-Leu152-Ile^153 in green. His56 is in blue and porphyrin
in white. These figures were drawn with Insight II (Biosym/MSI
Co.). The solvent front is at the left side of the iodine atom.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #2
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Title
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Pentacoordination of the heme iron of arthromyces ramosus peroxidase shown by a 1.8 a resolution crystallographic study at ph 4.5.
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Authors
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N.Kunishima,
F.Amada,
K.Fukuyama,
M.Kawamoto,
T.Matsunaga,
H.Matsubara.
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Ref.
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FEBS Lett, 1996,
378,
291-294.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Absorption spectra of ARP at different pH values. Left: in the presence of 1.4 M ammonium sulfate. Right: in its absence.
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The above figure is
reproduced from the cited reference
with permission from the Federation of European Biochemical Societies
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Secondary reference #3
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Title
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Crystal structures of cyanide- And triiodide-Bound forms of arthromyces ramosus peroxidase at different ph values. Perturbations of active site residues and their implication in enzyme catalysis.
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Authors
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K.Fukuyama,
N.Kunishima,
F.Amada,
T.Kubota,
H.Matsubara.
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Ref.
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J Biol Chem, 1995,
270,
21884-21892.
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PubMed id
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Secondary reference #4
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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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Secondary reference #5
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Title
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Crystallization and preliminary X-Ray diffraction studies of peroxidase from a fungus arthromyces ramosus.
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Authors
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N.Kunishima,
K.Fukuyama,
S.Wakabayashi,
M.Sumida,
M.Takaya,
Y.Shibano,
T.Amachi,
H.Matsubara.
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Ref.
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Proteins, 1993,
15,
216-220.
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PubMed id
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