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-
-
85069419176
-
-
FeSOD residues are named according to the numbering of E. coli FeSOD, and MnSOD residues, according to the numbering of E. coli MnSOD.
-
FeSOD residues are named according to the numbering of E. coli FeSOD, and MnSOD residues, according to the numbering of E. coli MnSOD.
-
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47
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85069425958
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Otwinowski, Z.; Minor, W. DENZO and SCALEPACK. In Crystallography of Biological Macromolecules; Rossmann, G., Arnold, E., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 2001; F, pp 226-235.
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-
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48
-
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3543012707
-
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Brünger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Crystallogr., Sect. D 1998, 54, 905-921.
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, vol.54
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-
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Brünger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
Read, R.J.11
Rice, L.M.12
Simonson, T.13
Warren, G.L.14
-
50
-
-
0030924992
-
-
Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallogr., Sect. D 1997, 53, 240-255.
-
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, pp. 240-255
-
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Murshudov, G.N.1
Vagin, A.A.2
Dodson, E.J.3
-
51
-
-
85069419816
-
-
LaMar, G. N. Spin Delocalization and Electronic Structure. In NMR of Paramagnetic Molecules; LaMar, G. N., Horrocks, W. D., Jr., Holm, R. H., Eds.; Academic Press: New York, 1973; pp 86-127.
-
LaMar, G. N. Spin Delocalization and Electronic Structure. In NMR of Paramagnetic Molecules; LaMar, G. N., Horrocks, W. D., Jr., Holm, R. H., Eds.; Academic Press: New York, 1973; pp 86-127.
-
-
-
-
54
-
-
85069421402
-
-
2+SOD as weak NMR resonances slightly offset from the main ones. These could reflect a small tendency of the His69 ring to adopt an alternate conformation in which the imidazole ring is flipped, or tautomerization.
-
2+SOD as weak NMR resonances slightly offset from the main ones. These could reflect a small tendency of the His69 ring to adopt an alternate conformation in which the imidazole ring is flipped, or tautomerization.
-
-
-
-
55
-
-
85069426017
-
-
2+SOD NMR line widths are greater than those observed for the other two variants, possibly as a reflection of slower electron spin relaxation.
-
2+SOD NMR line widths are greater than those observed for the other two variants, possibly as a reflection of slower electron spin relaxation.
-
-
-
-
56
-
-
85069424005
-
-
2+SOD). Resonance assignments for the mutant proteins are required before specific proposals can be made; however differences of comparable magnitude were observed upon ionization of Tyr34, indicating that they may be explained by changes in H-bonding and/or side chain packing.
-
2+SOD). Resonance assignments for the mutant proteins are required before specific proposals can be made; however differences of comparable magnitude were observed upon ionization of Tyr34, indicating that they may be explained by changes in H-bonding and/or side chain packing.
-
-
-
-
57
-
-
85069423129
-
-
We can distinguish S, 5/2 when each d orbital contains one unpaired electron and the ligand field is not strong, from S, 3/2 or 1/2 when there are more or stronger-field ligands
-
We can distinguish S = 5/2 when each d orbital contains one unpaired electron and the ligand field is not strong, from S = 3/2 or 1/2 when there are more or stronger-field ligands.
-
-
-
-
58
-
-
33751386251
-
-
Jacobsen, C. j. H.; Pedersen, E.; Villadsen, J.; Weihe, H. Inorg. Chem. 1993, 23 (7), 1216-1221.
-
(1993)
Inorg. Chem
, vol.23
, Issue.7
, pp. 1216-1221
-
-
Jacobsen, C.J.H.1
Pedersen, E.2
Villadsen, J.3
Weihe, H.4
-
60
-
-
85069424077
-
-
Coordination of Glu69 as a sixth ligand is excluded by our crystal structures. Yikilmaz, et al. Biochemistry 2006, 45, 1151-1161.
-
Coordination of Glu69 as a sixth ligand is excluded by our crystal structures. Yikilmaz, et al. Biochemistry 2006, 45, 1151-1161.
-
-
-
-
61
-
-
0028938504
-
-
Tierney, D. L.; Fee, J. A.; Ludwig, M. L.; Penner-Hahn, J. E. Biochemistry 1995, 34, 1661-1668.
-
(1995)
Biochemistry
, vol.34
, pp. 1661-1668
-
-
Tierney, D.L.1
Fee, J.A.2
Ludwig, M.L.3
Penner-Hahn, J.E.4
-
62
-
-
0030840839
-
-
Sorkin, D. L.; Duong, D. K.; Miller, A.-F. Biochemistry 1997, 36, 8202-8208.
-
(1997)
Biochemistry
, vol.36
, pp. 8202-8208
-
-
Sorkin, D.L.1
Duong, D.K.2
Miller, A.-F.3
-
64
-
-
0003121533
-
-
Fee, J. A.; McClune, G. J.; Lees, A. C.; Zidovetzki, R.; Pecht, I. Isr. J. Chem. 1981, 21, 54-58.
-
(1981)
Isr. J. Chem
, vol.21
, pp. 54-58
-
-
Fee, J.A.1
McClune, G.J.2
Lees, A.C.3
Zidovetzki, R.4
Pecht, I.5
-
65
-
-
85069425874
-
-
Detailed MCD, analyses of these mutants' Fe sites will be published separately
-
Detailed MCD, EPR, and computational analyses of these mutants' Fe sites will be published separately.
-
EPR, and computational
-
-
-
66
-
-
85069423343
-
-
Based on our experience with other mutants, it seems less likely that deprotonation of Tyr34 is occurring but not affecting any of the paramagnetically dispersed resonances.
-
Based on our experience with other mutants, it seems less likely that deprotonation of Tyr34 is occurring but not affecting any of the paramagnetically dispersed resonances.
-
-
-
-
67
-
-
85069421052
-
-
The rmsd between backbone heavy atoms of the 1.6 Å structure and the 1.1 Å structure is 0.4 Å.
-
The rmsd between backbone heavy atoms of the 1.6 Å structure and the 1.1 Å structure is 0.4 Å.
-
-
-
-
68
-
-
85069424931
-
-
Although we were not able to resolve discrete density for labile protons in the active site, aliphatic (nonexchangable) H atoms were visible on side chains in numerous areas of the structure
-
Although we were not able to resolve discrete density for labile protons in the active site, aliphatic (nonexchangable) H atoms were visible on side chains in numerous areas of the structure.
-
-
-
-
69
-
-
85069426653
-
-
Averaged over four sites per crystallographic unit cell
-
Averaged over four sites per crystallographic unit cell.
-
-
-
-
70
-
-
85069420429
-
-
4 structures were identified of which 2 were suspect.
-
4 structures were identified of which 2 were suspect.
-
-
-
-
72
-
-
85069422856
-
-
Carboxylates or carboxylic acids in which one O is H-bonded to water were identified in the Cambridge Structural Database. For 166 carboxylates receiving an H-bond from water, the average C-O distance for the H-bonded O was 1.24 Å (0.0L2) and the average C-O distance for the non-H-bonded O was 1.26 Å (0.012, These two distances are not significantly different, although there was a slight tendency for the O engaged in an H-bond to have a longer bond to C. In contrast, in 13 structures of neutral carboxylic acids donating an H-bond to water, the protonated O had an average C-O bond length that was 1.31 Å (0.015, more than 3 standard deviations longer than the double bonded C-O average distance of 1.22 Å 0.015, indicating localization of the double bond
-
Carboxylates or carboxylic acids in which one O is H-bonded to water were identified in the Cambridge Structural Database. For 166 carboxylates receiving an H-bond from water, the average C-O distance for the H-bonded O was 1.24 Å (0.0L2) and the average C-O distance for the non-H-bonded O was 1.26 Å (0.012). These two distances are not significantly different, although there was a slight tendency for the O engaged in an H-bond to have a longer bond to C. In contrast, in 13 structures of neutral carboxylic acids donating an H-bond to water, the protonated O had an average C-O bond length that was 1.31 Å (0.015), more than 3 standard deviations longer than the double bonded C-O average distance of 1.22 Å (0.015), indicating localization of the double bond.
-
-
-
-
73
-
-
85069419633
-
-
Glu 159 was chosen as a control on the basis of its excellent electron density and low B values.
-
Glu 159 was chosen as a control on the basis of its excellent electron density and low B values.
-
-
-
-
75
-
-
85069423876
-
-
In both models, Tyr34, Glu69, and coordinated solvent were neutral. In one, Tyr34's hydroxyl H was directed toward Glu69 to donate an H-bond; in the other, Tyr34's hydroxyl H was directed away from Glu69 and Tyr34 accepted an H-bond from Glu69.
-
In both models, Tyr34, Glu69, and coordinated solvent were neutral. In one, Tyr34's hydroxyl H was directed toward Glu69 to donate an H-bond; in the other, Tyr34's hydroxyl H was directed away from Glu69 and Tyr34 accepted an H-bond from Glu69.
-
-
-
-
76
-
-
85069421035
-
-
While the residue mutated derives from the second sphere, one interpretation of our results is that altered H-bonding resulting from the mutation in effect changes the nature of a first sphere residue, from more OH--like to more H2O-like
-
2O-like.
-
-
-
-
77
-
-
85069419311
-
-
It is reasonable that the nearby net-positively charged Fe center would disfavor protonation of His69
-
It is reasonable that the nearby net-positively charged Fe center would disfavor protonation of His69.
-
-
-
-
79
-
-
85069425660
-
-
m increases by 60 mV per unit decrease in pH.
-
m increases by 60 mV per unit decrease in pH.
-
-
-
-
80
-
-
85069423446
-
-
Q69E-Fe3+SOD's high affinity for a sixth ligand could represent effective long-range ionization of hydrated Glu69, via the equilibrium: Glu, H2O ↔ GluH, OH
-
-).
-
-
-
-
82
-
-
0029926948
-
-
5 April
-
Shan, S.; Loh, S.; Herschlag, D. Science 1996, 272 (5 April), 97-101.
-
(1996)
Science
, Issue.272
, pp. 97-101
-
-
Shan, S.1
Loh, S.2
Herschlag, D.3
-
83
-
-
85069423332
-
-
2+SOD we estimate a pK near 11. Both are consistent with experimental data on WT-FeSOD.
-
2+SOD we estimate a pK near 11. Both are consistent with experimental data on WT-FeSOD.
-
-
-
-
86
-
-
85069425992
-
-
This is consistent with the fact that Glu's intrinsic pK falls between those of water coordinated to Fe3+ and water coordinated to Fe2
-
2+.
-
-
-
-
87
-
-
85069424527
-
-
We do not place strong emphasis on energies calculated for restrained models because they were not fully optimized. However an optimized model of the Q69E-FeSOD active site yielded an Em 400 mV higher than that of WT-FeSOD when both oxidized states were assumed to be pentacoordinate, for ease of comparison. Thus, simplifed active sites are able to reproduce a large fraction of the observed elevation of Q69E-FeSOD's Em relative to WT-FeSOD, lending credibility to the computational results, in general
-
m relative to WT-FeSOD, lending credibility to the computational results, in general.
-
-
-
-
88
-
-
85069423155
-
-
However the free energy of dissociation of water must be taken into account when relating the energies of the two formulations
-
However the free energy of dissociation of water must be taken into account when relating the energies of the two formulations.
-
-
-
-
89
-
-
85069423811
-
-
Q69H-FeSOD was found to retain a WT-like active site structure [Yikilmaz, et al. Biochemistry 2006, 45, 1151-1161
-
Q69H-FeSOD was found to retain a WT-like active site structure [Yikilmaz, et al. Biochemistry 2006, 45, 1151-1161].
-
-
-
-
91
-
-
0028988431
-
-
Hammen, P. K.; Scholtz, J. M.; Anderson, J. W.; Waygood, E. B.; Klevit, R. E. Protein Sci. 1995, 4, 936-944.
-
(1995)
Protein Sci
, vol.4
, pp. 936-944
-
-
Hammen, P.K.1
Scholtz, J.M.2
Anderson, J.W.3
Waygood, E.B.4
Klevit, R.E.5
-
92
-
-
0028873117
-
-
Kiefer, L. L.; Paterno, S. A.; Fierke, C. A. J. Am. Chem. Soc. 1995, 117, 6831-6837.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 6831-6837
-
-
Kiefer, L.L.1
Paterno, S.A.2
Fierke, C.A.3
-
94
-
-
85069426906
-
-
m of Q69E-FeSOD.
-
m of Q69E-FeSOD.
-
-
-
-
95
-
-
85069424244
-
-
ox = 4.3, yielding 680 mV. More details are provided in the Supporting Information.
-
ox = 4.3, yielding 680 mV. More details are provided in the Supporting Information.
-
-
-
-
96
-
-
84962406568
-
-
Dey, A.; Hocking, R. K.; Larsen, P.; Borovik, A. S.; Hodgson, K. O.; Hedman, B.; Solomon, E. I. J. Am. Chem. Soc. 2006, 128, 9825-9833.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 9825-9833
-
-
Dey, A.1
Hocking, R.K.2
Larsen, P.3
Borovik, A.S.4
Hodgson, K.O.5
Hedman, B.6
Solomon, E.I.7
-
97
-
-
85069426187
-
-
m is proportional to the energy of the oxidized state minus that of the reduced state, of the active site.
-
m is proportional to the energy of the oxidized state minus that of the reduced state, of the active site.
-
-
-
-
98
-
-
85069421238
-
-
m by approximately 140 mV.
-
m by approximately 140 mV.
-
-
-
|