Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides

Shannon, R. D.

doi:10.1107/s0567739476001551

Cited by 57,953 publications

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“…All four carboxylate ligands are retained, and there are four solvent ligands, two more than for Mn II and Cd II , which is consistent for the coordination geometry of Sm III . The longer average metal-ligand distance in this structure compared to those in MnP-Mn II and MnP-Cd II also supports the presence of Sm III with an ionic radius of 1.08 Å in the octacoordinate state (42). The side chains of Glu39 and Arg42 are in only one conformation with the former in an open conformation and the latter in its compound I conformation.…”

Section: Resultssupporting

confidence: 58%

“…Hence, the Mn-binding site may accommodate metals with different ionic radii, provided the metals accept carboxylate ligands. The ionic radius of Mn II is 0.83 Å, and that of Cd II is 0.95 Å when hexacoordinated (42). There is evidence that Cd II can substitute for Mn II in other enzymes, such as photosystem II (43) Growth of MnP crystals in the absence of Mn II is severely affected, resulting in bleaching due to possible loss of heme at room temperature as observed for Mn II -free wild-type and mutant proteins (23).…”

Section: Resultsmentioning

confidence: 99%

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High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

et al. 2005

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Manganese peroxidase (MnP) is an extracellular heme enzyme that catalyzes the peroxidedependent oxidation of Mn II to Mn III . The Mn III is released from the enzyme in complex with oxalate. One heme propionate and the side chains of Glu35, Glu39, and Asp179 were identified as Mn II ligands in the 2.0 Å resolution crystal structure. The new 1.45 Å crystal structure of MnP complexed with Mn II provides a more accurate view of the Mn-binding site. New features include possible partial protonation of Glu39 in the Mn-binding site and glycosylation at Ser336. This is also the first report of MnPinhibitor complex structures. At the Mn-binding site, divalent Cd II exhibits octahedral, hexacoordinate ligation geometry similar to that of Mn II . Cd II also binds to a putative second weak metal-binding site with tetrahedral geometry at the C-terminus of the protein. Unlike that for Mn II and Cd II , coordination of trivalent Sm III at the Mn-binding site is octacoordinate. Sm III was removed from a MnP-Sm III crystal by soaking the crystal in oxalate and then reintroduced into the binding site. Thus, direct comparisons of Sm III -bound and metal-free structures were made using the same crystal. No ternary complex was observed upon incubation with oxalate. The reversible binding of Sm III may be a useful model for the reversible binding of Mn III to the enzyme, which is too unstable to allow similar examination.White-rot basidiomycetous fungi are the only organisms capable of degrading the phenylpropanoid, plant cell wall polymer, lignin (1-4). The lignin-degrading system of these fungi also can oxidize a variety of economically and environmentally important aromatic pollutants (5-9). Under ligninolytic conditions, the best-studied lignin-degrading fungus, Phanerochaete chrysosporium, secretes two families of extracellular heme peroxidases, lignin peroxidase (LiP) and manganese peroxidase (MnP) 1 (2-4, 10), and a hydrogen peroxide-generating system (2, 4, 6).MnP from P. chrysosporium has been studied extensively by a variety of biochemical and biophysical methods (11)(12)(13)(14)(15). The crystal structure illustrates that the heme environment of MnP is similar to that of other plant and fungal peroxidases (16). However, MnP is the only heme peroxidase capable of the one-electron oxidation of Mn II in a typical peroxidase reaction cycle:where MnPI and MnPII are the oxidized intermediates MnP compounds I and II, respectively. The 2.0 Å resolution crystal structure of MnP, determined at room temperature, shows that the substrate, Mn II , binds to one heme propionate and the side chains of three amino acids, Glu35, Glu39, and Asp179, as well as two solvent ligands (16) (Figure 1). This site was confirmed by kinetic and biophysical studies of wild-type MnP and of proteins containing point mutations in the putative binding site. † This research was supported by Grants GM42614 (to T.L.P.) and DK62524 (to M.S.) from the National Institutes of Health and Grants MCB-9808420 from the National Science Foundation and DE-03-9...

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Section: Resultssupporting

confidence: 58%

Section: Resultsmentioning

confidence: 99%

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

et al. 2005

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“…The sodium cation is smaller than K + as judged from crystal structures. Solid state structures show that the Na + , K + , and Cl -ions have diameters of 2.04, 3.02, and 3.62 Å, respectively [13]. In contrast, the calculated [14] hydrated diameters of these ions are: Na + = 5.98 Å, K + = 5.50 Å, and Cl -= 6.48 Å.…”

Section: The Challenge Presented By Group 1 (Alkali Metal) Cationsmentioning

confidence: 89%

Coordination and transport of alkali metal cations through phospholipid bilayer membranes by hydraphile channels

Gokel

Daschbach

2008

Coordination Chemistry Reviews

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Hydraphiles are synthetic ionophores that were designed to mimic some properties of protein channels that conduct such cations as sodium. They use macrocyclic (crown) polyethers as amphiphilic headgroups and as entry and exit portals. Their overall length is controlled by covalent links between the two headgroups (distal macrocycles) and the "central relay" unit, typically also an azacrown. The hydraphiles insert in the bilayer membranes of synthetic phospholipid vesicles or vital cells and mediate the transport of cations. The hydraphiles were intended to be models but they are functional channels. Because they are symmetric, they are non-rectifying but they show open-close behavior characteristic of natural channels. Because they are non-rectifying, when they insert into a microbial membrane, they lead to a rapid change in osmotic balance that proves fatal to bacteria.

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“…For instance, it is commonly accepted that a six-membered chelating ring (6m-CR) is preferred by small metal ions and they form stronger complexes when compared with a similar ligand that forms a five-membered chelating ring (5m-CR). 1,16,17 As a typical example one can consider ML complexes of small Be(II) (ionic radius 0.27 Å) 18 with NTPA (nitrilotri-3-propanoic acid) that has three 6m-CRs (log K 1 = 9.23 at 25 °C, μ = 0.5 M NaNO 3 ) 2 and NTA (nitrilotriacetic acid) that forms three 5m-CR (log K 1 = 7.79 at 25 °C, μ = 0.1 M KNO 3 ), 2 ∆log K 1 ≈ 1.4 in favor of the 6-membered-ring structure. Cd(II) can be regarded as a large metal ion (ionic radius 0.95 Å) 18 and log K 1 values of its ML complexes with NTPA and NTA are 3.4 (at 30 °C, μ = 0.1 M KNO 3 ) 2 and 9.76 (at 25 °C, μ = 0.1 M KNO 3 ), 2 respectively, ∆log K 1 ≈ 6.4 in favor of the 5-membered-ring structure.…”

Section: But This Does Not Apply To the Formation Constants Of Metalmentioning

confidence: 99%

“…1,16,17 As a typical example one can consider ML complexes of small Be(II) (ionic radius 0.27 Å) 18 with NTPA (nitrilotri-3-propanoic acid) that has three 6m-CRs (log K 1 = 9.23 at 25 °C, μ = 0.5 M NaNO 3 ) 2 and NTA (nitrilotriacetic acid) that forms three 5m-CR (log K 1 = 7.79 at 25 °C, μ = 0.1 M KNO 3 ), 2 ∆log K 1 ≈ 1.4 in favor of the 6-membered-ring structure. Cd(II) can be regarded as a large metal ion (ionic radius 0.95 Å) 18 and log K 1 values of its ML complexes with NTPA and NTA are 3.4 (at 30 °C, μ = 0.1 M KNO 3 ) 2 and 9.76 (at 25 °C, μ = 0.1 M KNO 3 ), 2 respectively, ∆log K 1 ≈ 6.4 in favor of the 5-membered-ring structure. This kind of large variations in formation constants is often attributed to geometrical properties (bite angles and bond lengths) 1,17 and crowded atoms in case of NTPA complexes with large metal ions.…”

Section: But This Does Not Apply To the Formation Constants Of Metalmentioning

confidence: 99%

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

Cukrowski

Govender

2010

Inorg. Chem.

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The log K 1 value of analytical quality was obtained for the NiNTPA complex using the DFTcomputed (at the B3LYP/6-311++G(d,p) level of theory in solvent, CPCM/UAKS) G (aq) values of the lowest energy conformers of the ligands, NTA (nitrilotriacetic acid) and NTPA (nitrilotri-3-propanoic acid), and Ni(II) complexes (NiNTA and NiNTPA). The described mathematical protocol is of general nature. The topological analysis, based on the Quantum Theory of Atoms in Molecules (QTAIM) of Bader, was used to characterize coordination bonds, chelating rings and additional intramolecular interactions in the complexes. The topological data, but not the structural analysis, explained the observed difference in stability of the NiNTA and NiNTPA complexes. It was found that the structural H···H contacts (classically regarded H-clashes, a steric hindrance destabilizing the complex) are in fact the H-H bonds contributing to the overall stability of NiNTPA. Also a CH-O bond was found in NiNTPA. The absence of intramolecular bonds between the atoms that fulfill a distance criterion in NiNTPA is explained by the formation of adjacent intramolecular rings that have larger electron density at the ring critical points when compared with the rings containing these atoms. It is postulated that the strength of a chelating ring (a chelating effect) can be measured by the electron density at the ring critical point. It was found that the strain energy, E s , in the as-in-complex NTPA ligand (E s is significantly lowered by the presence of the intramolecular bonded interactions found by QTAIM) is responsible for the decrease in strength of NiNTPA; the E s ratio (NTPA/NTA) of 1.9 correlates well with the experimental log K 1 ratio (NTA/NTPA) of 1.98.2

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Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides

Cited by 57,953 publications

References 17 publications

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

Coordination and transport of alkali metal cations through phospholipid bilayer membranes by hydraphile channels

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

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Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides

Cited by 57,953 publications

References 17 publications

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes,

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes,

Coordination and transport of alkali metal cations through phospholipid bilayer membranes by hydraphile channels

A Density Functional Theory- and Atoms in Molecules-based Study of NiNTA and NiNTPA Complexes toward Physical Properties Controlling their Stability. A New Method of Computing a Formation Constant

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High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,