Crystal Structure of a Thermostable Alanine Racemase from Thermoanaerobacter tengcongensis MB4 Reveals the Role of Gln360 in Substrate Selection

The electronic structure of a series perovskites ABX3 (A = Cs; B = Ca, Sr, and Ba; X = F, Cl, Br, and I) in the presence and absence of antisite defect XB were systematically investigated based on density-functional-theory calculations. Both cubic and orthorhombic perovskites were considered. It was observed that for certain perovskite compositions and crystal structure, presence of antisite point defect leads to the formation of electronic defect state(s) within the band gap. We showed that both the type of electronic defect states and their individual energy level location within the bandgap can be predicted based on easily available intrinsic properties of the constituent elements, such as the bond-dissociation energy of the B–X and X–X bond, the X–X covalent bond length, and the atomic size of halide (X) as well as structural characteristic such as B–X–B bond angle. Overall, this work provides a science-based generic principle to design the electronic states within the band structure in Cs-based perovskites in presence of point defects such as antisite defect.

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The role of silver in the crystal structure of pyrargyrite: single crystal X-ray diffraction study

Journal of Geosciences ◽

10.3190/jgeosci.067 ◽

2012 ◽

pp. 161-167 ◽

Cited By ~ 2

Author(s):

F. Laufek ◽

J. Sejkora ◽

M. Dušek

Keyword(s):

Crystal Structure ◽

Single Crystal ◽

Diffraction Study ◽

X Ray Diffraction ◽

X Ray

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Crystal structures of Ca2+–calmodulin bound to NaV C-terminal regions suggest role for EF-hand domain in binding and inactivation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818618116 ◽

2019 ◽

Vol 116 (22) ◽

pp. 10763-10772 ◽

Cited By ~ 10

Author(s):

Bernd R. Gardill ◽

Ricardo E. Rivera-Acevedo ◽

Ching-Chieh Tung ◽

Filip Van Petegem

Keyword(s):

Crystal Structure ◽

Binding Sites ◽

Binding Mode ◽

Conformational Switch ◽

Channel Inactivation ◽

Dependent Inactivation ◽

Ef Hand ◽

Inherited Arrhythmia ◽

A Site

Voltage-gated sodium (NaV) and calcium channels (CaV) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca2+-occupied CaM, bound to the CT of NaV1.5. The structure shows that the C-terminal lobe binds to a site ∼90° rotated relative to a previous site reported for an apoCaM complex with the NaV1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca2+-occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca2+-free and Ca2+-occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related NaV1.4 channel has been shown to undergo Ca2+-dependent inactivation (CDI) akin to CaVs. We present a crystal structure of Ca2+/CaM bound to the NaV1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.

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Spotlight on Alkali Metals: The Structural Chemistry of Alkali Metal Thallides

Crystals ◽

10.3390/cryst10111013 ◽

2020 ◽

Vol 10 (11) ◽

pp. 1013

Author(s):

Stefanie Gärtner

Keyword(s):

Crystal Structure ◽

Alkali Metal ◽

Crystal Structures ◽

Alkali Metals ◽

Valence Electron ◽

Oxidation States ◽

Valence Electron Concentration ◽

Base Metals ◽

Charge Balancing

Alkali metal thallides go back to the investigative works of Eduard Zintl about base metals in negative oxidation states. In 1932, he described the crystal structure of NaTl as the first representative for this class of compounds. Since then, a bunch of versatile crystal structures has been reported for thallium as electronegative element in intermetallic solid state compounds. For combinations of thallium with alkali metals as electropositive counterparts, a broad range of different unique structure types has been observed. Interestingly, various thallium substructures at the same or very similar valence electron concentration (VEC) are obtained. This in return emphasizes that the role of the alkali metals on structure formation goes far beyond ancillary filling atoms, which are present only due to charge balancing reasons. In this review, the alkali metals are in focus and the local surroundings of the latter are discussed in terms of their crystallographic sites in the corresponding crystal structures.

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Role of electronic factors in the formation of anionic complexes of tellurium(IV): Crystal structure of bis(4-methylbenzoylmethyltriphenylphosphonium) hexabromotellurate(IV)

Polyhedron ◽

10.1016/j.poly.2005.07.038 ◽

2006 ◽

Vol 25 (3) ◽

pp. 747-752

Author(s):

Ashok K.S. Chauhan ◽

Arun Kumar ◽

Shobhit Charan ◽

Ramesh C. Srivastava ◽

Ray J. Butcher

Keyword(s):

Crystal Structure ◽

Anionic Complexes

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Crystal Structure of Type 1 Ribonuclease H from Hyperthermophilic ArchaeonSulfolobus tokodaii: Role of Arginine 118 and C-Terminal Anchoring†,‡

Biochemistry ◽

10.1021/bi700830f ◽

2007 ◽

Vol 46 (41) ◽

pp. 11494-11503 ◽

Cited By ~ 20

Author(s):

Dong-Ju You ◽

Hyongi Chon ◽

Yuichi Koga ◽

Kazufumi Takano ◽

Shigenori Kanaya

Keyword(s):

Crystal Structure ◽

Ribonuclease H

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Crystal structure of the wild-type and D30A mutant thioredoxin h of Chlamydomonas reinhardtii and implications for the catalytic mechanism

Biochemical Journal ◽

10.1042/bj3590065 ◽

2001 ◽

Vol 359 (1) ◽

pp. 65-75 ◽

Cited By ~ 25

Author(s):

Valeria MENCHISE ◽

Catherine CORBIER ◽

Claude DIDIERJEAN ◽

Michele SAVIANO ◽

Ettore BENEDETTI ◽

...

Keyword(s):

Crystal Structure ◽

Proton Transfer ◽

Chlamydomonas Reinhardtii ◽

Catalytic Mechanism ◽

Structural Data ◽

Careful Analysis ◽

Wild Type ◽

Thioredoxin H ◽

Dynamics Simulations

Thioredoxins are ubiquitous proteins which catalyse the reduction of disulphide bridges on target proteins. The catalytic mechanism proceeds via a mixed disulphide intermediate whose breakdown should be enhanced by the involvement of a conserved buried residue, Asp-30, as a base catalyst towards residue Cys-39. We report here the crystal structure of wild-type and D30A mutant thioredoxin h from Chlamydomonas reinhardtii, which constitutes the first crystal structure of a cytosolic thioredoxin isolated from a eukaryotic plant organism. The role of residue Asp-30 in catalysis has been revisited since the distance between the carboxylate OD1 of Asp-30 and the sulphur SG of Cys-39 is too great to support the hypothesis of direct proton transfer. A careful analysis of all available crystal structures reveals that the relative positioning of residues Asp-30 and Cys-39 as well as hydrophobic contacts in the vicinity of residue Asp-30 do not allow a conformational change sufficient to bring the two residues close enough for a direct proton transfer. This suggests that protonation/deprotonation of Cys-39 should be mediated by a water molecule. Molecular-dynamics simulations, carried out either in vacuo or in water, as well as proton-inventory experiments, support this hypothesis. The results are discussed with respect to biochemical and structural data.

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Synthesis, Crystal Structure and DFT Study of a Dinuclear Cu 1 Complex With (E)-2-Benzylidene-N-Methylhydrazinecarbothioamide: Role of Halogen-Hydrogen Bonds in Copper-Copper Bridge Bonding

SSRN Electronic Journal ◽

10.2139/ssrn.3639525 ◽

2020 ◽

Author(s):

Tarlok S. Lobana

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Dft Study

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The crystal structure of Mycobacterium tuberculosis high-temperature requirement A protein reveals an autoregulatory mechanism

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x18016217 ◽

2018 ◽

Vol 74 (12) ◽

pp. 803-809

Author(s):

Arvind Kumar Gupta ◽

Debashree Behera ◽

Balasubramanian Gopal

Keyword(s):

Crystal Structure ◽

Mycobacterium Tuberculosis ◽

High Temperature ◽

Catalytic Domain ◽

Pdz Domain ◽

Regulatory Pathways ◽

Inactive Conformation ◽

Temperature Requirement ◽

Autoregulatory Mechanism

The crystal structure of Mycobacterium tuberculosis high-temperature requirement A (HtrA) protein was determined at 1.83 Å resolution. This membrane-associated protease is essential for the survival of M. tuberculosis. The crystal structure reveals that interactions between the PDZ domain and the catalytic domain in HtrA lead to an inactive conformation. This finding is consistent with its proposed role as a regulatory protease that is conditionally activated upon appropriate environmental triggers. The structure provides a basis for directed studies to evaluate the role of this essential protein and the regulatory pathways that are influenced by this protease.

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Effects of dietary alteration of bicarbonate and magnesium on rat bone

AJP Renal Physiology ◽

10.1152/ajprenal.1986.250.2.f302 ◽

1986 ◽

Vol 250 (2) ◽

pp. F302-F307 ◽

Cited By ~ 4

Author(s):

J. M. Burnell ◽

C. Liu ◽

A. G. Miller ◽

E. Teubner

Keyword(s):

Crystal Structure ◽

Bone Formation ◽

X Ray Diffraction ◽

X Ray ◽

Growing Rats ◽

Final Composition ◽

Rat Bone

To study the effects of bicarbonate and magnesium on bone, mild acidosis and/or hypermagnesemia were produced in growing rats by feeding ammonium chloride and/or magnesium sulfate. Bone composition, quantitative histomorphometry, and mineral x-ray diffraction (XRD) characteristics were measured after 6 wk of treatment. The results demonstrated that both acidosis (decreased HCO3) and hypermagnesemia inhibited periosteal bone formation, and, when combined, results were summative; and the previously observed in vitro role of HCO3- and Mg2+ as inhibitors of crystal growth were confirmed in vivo. XRD measurements demonstrated that decreased plasma HCO3 resulted in larger crystals and increased Mg resulted in smaller crystals. However, the combined XRD effects of acidosis and hypermagnesemia resembled acidosis alone. It is postulated that the final composition and crystal structure of bone are strongly influenced by HCO3- and Mg2+, and the effects are mediated by the combined influence on both osteoblastic bone formation and the growth of hydroxyapatite.

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