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PDBsum entry 5ngx
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Oxidoreductase
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PDB id
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5ngx
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References listed in PDB file
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Key reference
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Title
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Distinguishing nitro vs nitrito coordination in cytochrome c' Using vibrational spectroscopy and density functional theory.
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Authors
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Z.N.Nilsson,
B.L.Mandella,
K.Sen,
D.Kekilli,
M.A.Hough,
P.Moënne-Loccoz,
R.W.Strange,
C.R.Andrew.
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Ref.
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Inorg Chem, 2017,
56,
13205-13213.
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PubMed id
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Abstract
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Nitrite coordination to heme cofactors is a key step in the anaerobic production
of the signaling molecule nitric oxide (NO). An ambidentate ligand, nitrite has
the potential to coordinate via the N- (nitro) or O- (nitrito) atoms in a manner
that can direct its reactivity. Distinguishing nitro vs nitrito coordination,
along with the influence of the surrounding protein, is therefore of particular
interest. In this study, we probed Fe(III) heme-nitrite coordination in
Alcaligenes xylosoxidans cytochrome c' (AXCP), an NO carrier that excludes
anions in its native state but that readily binds nitrite (Kd∼ 0.5
mM) following a distal Leu16 → Gly mutation to remove distal steric
constraints. Room-temperature resonance Raman spectra (407 nm excitation)
identify ν(Fe-NO2), δ(ONO), and νs(NO2)
nitrite ligand vibrations in solution. Illumination with 351 nm UV light results
in photoconversion to {FeNO}6and {FeNO}7states, enabling
FTIR measurements to distinguish νs(NO2) and
νas(NO2) vibrations from differential spectra. Density
functional theory calculations highlight the connections between heme
environment, nitrite coordination mode, and vibrational properties and confirm
that nitrite binds to L16G AXCP exclusively through the N atom. Efforts to
obtain the nitrite complex crystal structure were hampered by photochemistry in
the X-ray beam. Although low dose crystal structures could be modeled with a
mixed nitrite (nitro)/H2O distal population, their photosensitivity
and partial occupancy underscores the value of the vibrational approach.
Overall, this study sheds light on steric determinants of heme-nitrite binding
and provides vibrational benchmarks for future studies of heme protein nitrite
reactions.
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