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PDBsum entry 1mbo
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Oxygen storage
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PDB id
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1mbo
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* Residue conservation analysis
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Enzyme class 2:
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E.C.1.11.1.-
- ?????
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Enzyme class 3:
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E.C.1.7.-.-
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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DOI no:
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J Mol Biol
142:531-554
(1980)
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PubMed id:
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Structure and refinement of oxymyoglobin at 1.6 A resolution.
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S.E.Phillips.
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ABSTRACT
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Selected figure(s)
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Figure 1.
FIG. 1. Stereo diagram of the polypeptide chain in Mb&. The helical regions are labelled
B to H, and every fourth , is marked. The haem-oxygen complex, and side-chains for PhelCD,
His'lE, ValllE, Hi&F and Tyr23H are shown with thinner bonds Broken lines indicate hydrogen
Donds. A bound sulphate ion lies at the N-terminal end of helix E.
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Figure 13.
FIG. 13. Histogram of contact distances between polr side-chain atoms and water molecules in
the first hydration shell.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1980,
142,
531-554)
copyright 1980.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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T.Kuwada,
T.Hasegawa,
T.Takagi,
T.Sakae,
I.Sato,
and
F.Shishikura
(2011).
Involvement of the distal Arg residue in Cl⁻ binding of midge larval haemoglobin.
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Acta Crystallogr D Biol Crystallogr,
67,
488-495.
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PDB codes:
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N.Bergmann,
S.Bonhommeau,
K.M.Lange,
S.M.Greil,
S.Eisebitt,
F.de Groot,
M.Chergui,
and
E.F.Aziz
(2010).
On the enzymatic activity of catalase: an iron L-edge X-ray absorption study of the active centre.
|
| |
Phys Chem Chem Phys,
12,
4827-4832.
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T.D.Fenn,
M.J.Schnieders,
and
A.T.Brunger
(2010).
A smooth and differentiable bulk-solvent model for macromolecular diffraction.
|
| |
Acta Crystallogr D Biol Crystallogr,
66,
1024-1031.
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T.Kuwada,
T.Hasegawa,
T.Takagi,
I.Sato,
and
F.Shishikura
(2010).
pH-dependent structural changes in haemoglobin component V from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera).
|
| |
Acta Crystallogr D Biol Crystallogr,
66,
258-267.
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PDB codes:
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A.T.Brunger,
B.Delabarre,
J.M.Davies,
and
W.I.Weis
(2009).
X-ray structure determination at low resolution.
|
| |
Acta Crystallogr D Biol Crystallogr,
65,
128-133.
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J.Praaenikar,
P.V.Afonine,
G.Guncar,
P.D.Adams,
and
D.Turk
(2009).
Averaged kick maps: less noise, more signal... and probably less bias.
|
| |
Acta Crystallogr D Biol Crystallogr,
65,
921-931.
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J.F.Storz,
and
H.Moriyama
(2008).
Mechanisms of hemoglobin adaptation to high altitude hypoxia.
|
| |
High Alt Med Biol,
9,
148-157.
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A.T.Brunger
(2007).
Version 1.2 of the Crystallography and NMR system.
|
| |
Nat Protoc,
2,
2728-2733.
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J.F.Storz,
S.J.Sabatino,
F.G.Hoffmann,
E.J.Gering,
H.Moriyama,
N.Ferrand,
B.Monteiro,
and
M.W.Nachman
(2007).
The molecular basis of high-altitude adaptation in deer mice.
|
| |
PLoS Genet,
3,
e45.
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T.J.Oldfield
(2007).
CAALIGN: a program for pairwise and multiple protein-structure alignment.
|
| |
Acta Crystallogr D Biol Crystallogr,
63,
514-525.
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H.Nakashima,
J.Y.Hasegawa,
and
H.Nakatsuji
(2006).
On the reversible O2 binding of the Fe-porphyrin complex.
|
| |
J Comput Chem,
27,
426-433.
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H.Nakashima,
J.Y.Hasegawa,
and
H.Nakatsuji
(2006).
On the O2 binding of Fe-porphyrin, Fe-porphycene, and Fe-corrphycene complexes.
|
| |
J Comput Chem,
27,
1363-1372.
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R.A.Goldbeck,
S.Bhaskaran,
C.Ortega,
J.L.Mendoza,
J.S.Olson,
J.Soman,
D.S.Kliger,
and
R.M.Esquerra
(2006).
Water and ligand entry in myoglobin: assessing the speed and extent of heme pocket hydration after CO photodissociation.
|
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Proc Natl Acad Sci U S A,
103,
1254-1259.
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A.Karlsson,
J.V.Parales,
R.E.Parales,
D.T.Gibson,
H.Eklund,
and
S.Ramaswamy
(2005).
NO binding to naphthalene dioxygenase.
|
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J Biol Inorg Chem,
10,
483-489.
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PDB codes:
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J.T.Lecomte,
D.A.Vuletich,
and
A.M.Lesk
(2005).
Structural divergence and distant relationships in proteins: evolution of the globins.
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Curr Opin Struct Biol,
15,
290-301.
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P.V.Afonine,
R.W.Grosse-Kunstleve,
and
P.D.Adams
(2005).
A robust bulk-solvent correction and anisotropic scaling procedure.
|
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Acta Crystallogr D Biol Crystallogr,
61,
850-855.
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T.D.Pfister,
T.Ohki,
T.Ueno,
I.Hara,
S.Adachi,
Y.Makino,
N.Ueyama,
Y.Lu,
and
Y.Watanabe
(2005).
Monooxygenation of an aromatic ring by F43W/H64D/V68I myoglobin mutant and hydrogen peroxide. Myoglobin mutants as a model for P450 hydroxylation chemistry.
|
| |
J Biol Chem,
280,
12858-12866.
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W.E.Royer,
H.Zhu,
T.A.Gorr,
J.F.Flores,
and
J.E.Knapp
(2005).
Allosteric hemoglobin assembly: diversity and similarity.
|
| |
J Biol Chem,
280,
27477-27480.
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E.Martineau,
P.J.L'Heureux,
and
J.R.Gunn
(2004).
Biased fragment distribution in MC simulation of protein folding.
|
| |
J Comput Chem,
25,
1895-1903.
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M.W.Vetting,
L.P.Wackett,
L.Que,
J.D.Lipscomb,
and
D.H.Ohlendorf
(2004).
Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.
|
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J Bacteriol,
186,
1945-1958.
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PDB codes:
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R.J.Morris,
E.Blanc,
and
G.Bricogne
(2004).
On the interpretation and use of <|E|2>(d*) profiles.
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Acta Crystallogr D Biol Crystallogr,
60,
227-240.
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K.Karbstein,
and
D.Herschlag
(2003).
Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function.
|
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Proc Natl Acad Sci U S A,
100,
2300-2305.
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S.Kundu,
and
M.S.Hargrove
(2003).
Distal heme pocket regulation of ligand binding and stability in soybean leghemoglobin.
|
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Proteins,
50,
239-248.
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A.Fokine,
and
A.Urzhumtsev
(2002).
Flat bulk-solvent model: obtaining optimal parameters.
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Acta Crystallogr D Biol Crystallogr,
58,
1387-1392.
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A.V.Barzykin,
K.Seki,
and
M.Tachiya
(2001).
Kinetics of diffusion-assisted reactions in microheterogeneous systems.
|
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Adv Colloid Interface Sci,
89,
47.
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B.Stec,
and
G.N.Phillips
(2001).
How the CO in myoglobin acquired its bend: lessons in interpretation of crystallographic data.
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Acta Crystallogr D Biol Crystallogr,
57,
751-754.
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W.E.Royer,
J.E.Knapp,
K.Strand,
and
H.A.Heaslet
(2001).
Cooperative hemoglobins: conserved fold, diverse quaternary assemblies and allosteric mechanisms.
|
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Trends Biochem Sci,
26,
297-304.
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C.Rovira,
and
M.Parrinello
(2000).
Harmonic and anharmonic dynamics of Fe-CO and Fe-O(2) in heme models.
|
| |
Biophys J,
78,
93.
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G.Evans,
P.Roversi,
and
G.Bricogne
(2000).
In-house low-resolution X-ray crystallography.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
1304-1311.
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H.Kikuchi,
H.Wako,
K.Yura,
M.Go,
and
M.Mimuro
(2000).
Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis.
|
| |
Biophys J,
79,
1587-1600.
|
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M.Flores,
E.Wajnberg,
and
G.Bemski
(2000).
Proton electron nuclear double resonance from nitrosyl horse heart myoglobin: the role of His-E7 and Val-E11.
|
| |
Biophys J,
78,
2107-2115.
|
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Y.Isogai,
A.Ishii,
T.Fujisawa,
M.Ota,
and
K.Nishikawa
(2000).
Redesign of artificial globins: effects of residue replacements at hydrophobic sites on the structural properties.
|
| |
Biochemistry,
39,
5683-5690.
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B.Yu,
M.Blaber,
A.M.Gronenborn,
G.M.Clore,
and
D.L.Caspar
(1999).
Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography.
|
| |
Proc Natl Acad Sci U S A,
96,
103-108.
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PDB code:
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H.Shimada,
S.Nagano,
Y.Ariga,
M.Unno,
T.Egawa,
T.Hishiki,
Y.Ishimura,
F.Masuya,
T.Obata,
and
H.Hori
(1999).
Putidaredoxin-cytochrome p450cam interaction. Spin state of the heme iron modulates putidaredoxin structure.
|
| |
J Biol Chem,
274,
9363-9369.
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J.Vojtechovský,
K.Chu,
J.Berendzen,
R.M.Sweet,
and
I.Schlichting
(1999).
Crystal structures of myoglobin-ligand complexes at near-atomic resolution.
|
| |
Biophys J,
77,
2153-2174.
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PDB codes:
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M.Ramin,
W.Shepard,
R.Fourme,
and
R.Kahn
(1999).
Multiwavelength anomalous solvent contrast (MASC): derivation of envelope structure-factor amplitudes and comparison with model values.
|
| |
Acta Crystallogr D Biol Crystallogr,
55,
157-167.
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PDB codes:
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Y.Isogai,
M.Ota,
T.Fujisawa,
H.Izuno,
M.Mukai,
H.Nakamura,
T.Iizuka,
and
K.Nishikawa
(1999).
Design and synthesis of a globin fold.
|
| |
Biochemistry,
38,
7431-7443.
|
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F.Nastri,
A.Lombardi,
L.D.D'Andrea,
M.Sanseverino,
O.Maglio,
and
V.Pavone
(1998).
Miniaturized hemoproteins.
|
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Biopolymers,
47,
5.
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S.Della Longa,
S.Pin,
R.Cortès,
A.V.Soldatov,
and
B.Alpert
(1998).
Fe-heme conformations in ferric myoglobin.
|
| |
Biophys J,
75,
3154-3162.
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Y.Yamamoto,
T.Nakashima,
E.Kawano,
and
R.Chûjô
(1998).
1H-NMR investigation of the influence of the heme orientation on functional properties of myoglobin.
|
| |
Biochim Biophys Acta,
1388,
349-362.
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Y.Zhao,
C.Hoganson,
G.T.Babcock,
and
M.A.Marletta
(1998).
Structural changes in the heme proximal pocket induced by nitric oxide binding to soluble guanylate cyclase.
|
| |
Biochemistry,
37,
12458-12464.
|
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A.Cupane,
M.Leone,
V.Militello,
F.K.Friedman,
A.P.Koley,
G.B.Vasquez,
W.S.Brinigar,
M.Karavitis,
and
C.Fronticelli
(1997).
Modification of alpha-chain or beta-chain heme pocket polarity by Val(E11) --> thr substitution has different effects on the steric, dynamic, and functional properties of human recombinant hemoglobin. Deoxy derivatives.
|
| |
J Biol Chem,
272,
26271-26278.
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D.Wang,
U.Kreutzer,
Y.Chung,
and
T.Jue
(1997).
Myoglobin and hemoglobin rotational diffusion in the cell.
|
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Biophys J,
73,
2764-2770.
|
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E.Fernandez,
A.Duke,
I.Sevrioukova,
and
R.V.Shohet
(1997).
Analysis of the myoglobin gene in heart disease.
|
| |
Hum Mutat,
9,
426-430.
|
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G.S.Lukat-Rodgers,
and
K.R.Rodgers
(1997).
Characterization of ferrous FixL-nitric oxide adducts by resonance Raman spectroscopy.
|
| |
Biochemistry,
36,
4178-4187.
|
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L.M.Miller,
A.J.Pedraza,
and
M.R.Chance
(1997).
Identification of conformational substates involved in nitric oxide binding to ferric and ferrous myoglobin through difference Fourier transform infrared spectroscopy (FTIR).
|
| |
Biochemistry,
36,
12199-12207.
|
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O.Galkin,
S.Buchter,
A.Tabirian,
and
A.Schulte
(1997).
Pressure effects on the proximal heme pocket in myoglobin probed by Raman and near-infrared absorption spectroscopy.
|
| |
Biophys J,
73,
2752-2763.
|
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S.Bhattacharya,
S.F.Sukits,
K.L.MacLaughlin,
and
J.T.Lecomte
(1997).
The tautomeric state of histidines in myoglobin.
|
| |
Biophys J,
73,
3230-3240.
|
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T.Uchida,
K.Ishimori,
and
I.Morishima
(1997).
The effects of heme pocket hydrophobicity on the ligand binding dynamics in myoglobin as studied with leucine 29 mutants.
|
| |
J Biol Chem,
272,
30108-30114.
|
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|
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T.Uchida,
M.Unno,
K.Ishimori,
and
I.Morishima
(1997).
Effects of the intramolecular disulfide bond on ligand binding dynamics in myoglobin.
|
| |
Biochemistry,
36,
324-332.
|
|
|
|
|
|
|
T.Y.Teng,
V.Srajer,
and
K.Moffat
(1997).
Initial trajectory of carbon monoxide after photodissociation from myoglobin at cryogenic temperatures.
|
| |
Biochemistry,
36,
12087-12100.
|
|
|
|
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|
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Y.Shirakihara,
A.G.Leslie,
J.P.Abrahams,
J.E.Walker,
T.Ueda,
Y.Sekimoto,
M.Kambara,
K.Saika,
Y.Kagawa,
and
M.Yoshida
(1997).
The crystal structure of the nucleotide-free alpha 3 beta 3 subcomplex of F1-ATPase from the thermophilic Bacillus PS3 is a symmetric trimer.
|
| |
Structure,
5,
825-836.
|
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PDB code:
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B.Giardina,
P.Ascenzi,
M.E.Clementi,
G.De Sanctis,
M.Rizzi,
and
M.Coletta
(1996).
Functional modulation by lactate of myoglobin. A monomeric allosteric hemoprotein.
|
| |
J Biol Chem,
271,
16999-17001.
|
|
|
|
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|
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E.A.Brucker,
J.S.Olson,
G.N.Phillips,
Y.Dou,
and
M.Ikeda-Saito
(1996).
High resolution crystal structures of the deoxy, oxy, and aquomet forms of cobalt myoglobin.
|
| |
J Biol Chem,
271,
25419-25422.
|
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PDB codes:
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E.Lloyd,
D.L.Burk,
J.C.Ferrer,
R.Maurus,
J.Doran,
P.R.Carey,
G.D.Brayer,
and
A.G.Mauk
(1996).
Electrostatic modification of the active site of myoglobin: characterization of the proximal Ser92Asp variant.
|
| |
Biochemistry,
35,
11901-11912.
|
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PDB code:
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A.M.Mathiowetz,
and
W.A.Goddard
(1995).
Building proteins from C alpha coordinates using the dihedral probability grid Monte Carlo method.
|
| |
Protein Sci,
4,
1217-1232.
|
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D.A.Bisig,
E.E.Di Iorio,
K.Diederichs,
K.H.Winterhalter,
and
K.Piontek
(1995).
Crystal structure of Asian elephant (Elephas maximus) cyano-metmyoglobin at 1.78-A resolution. Phe29(B10) accounts for its unusual ligand binding properties.
|
| |
J Biol Chem,
270,
20754-20762.
|
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PDB code:
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G.N.Phillips,
and
B.M.Pettitt
(1995).
Structure and dynamics of the water around myoglobin.
|
| |
Protein Sci,
4,
149-158.
|
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|
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H.H.Lai,
T.Li,
D.S.Lyons,
G.N.Phillips,
J.S.Olson,
and
Q.H.Gibson
(1995).
Phe-46(CD4) orients the distal histidine for hydrogen bonding to bound ligands in sperm whale myoglobin.
|
| |
Proteins,
22,
322-339.
|
|
|
PDB codes:
|
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|
|
M.Brunori
(1995).
The renaissance of myoglobin: dynamics, structure and oxygen binding control.
|
| |
Experientia,
51,
204.
|
|
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|
|
R.Srinivasan,
and
G.D.Rose
(1995).
LINUS: a hierarchic procedure to predict the fold of a protein.
|
| |
Proteins,
22,
81-99.
|
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|
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U.Ermler,
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