Crystal structures ofBacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+

Author(s):  
Michael B. Berry ◽  
George N. Phillips
2001 ◽  
Vol 79 (3) ◽  
pp. 263-271
Author(s):  
Paul K Baker ◽  
Michael GB Drew ◽  
Deborah S Evans

Reaction of [WI2(CO)3(NCMe)2] with two equivalents of 1-phenyl-1-propyne (MeC2Ph) in CH2Cl2, and in the absence of light, gave the bis(1-phenyl-1-propyne) complex [WI2(CO)(NCMe)(η2-MeC2Ph)2] (1) in 77% yield. Treatment of equimolar quantities of 1 and NCR (R = Et, i-Pr, t-Bu, Ph) in CH2Cl2 afforded the nitrile-exchanged products, [WI2(CO)(NCR)(η2-MeC2Ph)2] (2-5) (R = Et (2), i-Pr (3), t-Bu (4), Ph (5)). Complexes 1, 2, and 5 were structurally characterized by X-ray crystallography. All three structures have the same pseudo-octahedral geometry, with the equatorial sites being occupied by cis and parallel alkyne groups, which are trans to the cis-iodo groups. The trans carbon monoxide and acetonitrile ligands occupy the axial sites. In structures 1 and 2, the methyl and phenyl substituents of the 1-phenyl-1-propyne ligands are cis to each other, whereas for the bulkier NCPh complex (5), the methyl and phenyl groups are trans to one another. This is the first time that this arrangement has been observed in the solid state in bis(alkyne) complexes of this type.Key words: bis(1-phenyl-1-propyne), carbonyl, nitrile, diiodo, tungsten(II), crystal structures.


2014 ◽  
Vol 70 (11) ◽  
pp. 1468-1471
Author(s):  
Trung Thanh Thach ◽  
Sangho Lee

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groupsP21andP1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space groupC2, with unit-cell parametersa= 73.5,b= 54.3,c= 62.7 Å, β = 118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cαatoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitorP1,P5-bis(adenosine-5′-)pentaphosphate (Ap5A) belonged to space groupP1, with unit-cell parametersa= 53.9,b= 62.3,c= 63.0 Å, α = 101.9, β = 112.6, γ = 89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.


2009 ◽  
Vol 65 (a1) ◽  
pp. s170-s170
Author(s):  
A. Mukhopaadhyay ◽  
A. V. Kladova ◽  
J. Trincão ◽  
S. A. Bursakov ◽  
I. Moura ◽  
...  

2014 ◽  
Vol 7 (1) ◽  
pp. 15-19 ◽  
Author(s):  
Danica Čechová ◽  
Alena Martišková ◽  
Jan Moncol

Abstract The crystal structures of the title compounds, [Mn(phen)2Cl2] (I) and [Mn(bipy)2Cl2] (II), have been determined at 150 K. The manganese atoms in both compounds are coordinated by four pyridine nitrogen atoms from two 1,10-phenanthroline or 4,4´-bipyridine ligands and two chloride anions, resulting in a distorted cis-MnN4Cl2 octahedral geometry. Both complexes are connected through C-H・・・Cl hydrogen bonds into frameworks. The π-π stacking interactions are observed in crystal structure of both ones.


1999 ◽  
Vol 54 (12) ◽  
pp. 1563-1567 ◽  
Author(s):  
Evgeni V. Avtomonov ◽  
Konstantin A. Rufanov

Reaction of 3 equivalents of ZrCl4 · 2Et2O (1) with 1 equivalent of (Et2N4Zr in diethyl ether readily affords crystalline (Et2N)ZrCl3 · 2Et2O (2) in almost quantitative yield. The product was characterised by elemental analysis and by 1H. 13 C NMR, and MS techniques. The reactivity of this reagent towards C-H acidic compounds has been studied using cyclopentadiene as a C-H acid. The crystal structures of both 1 and 2 have been determined by X-ray diffractometry. The coordination polyhedra reveal a nearly perfect octahedral geometry with a trans Et2O ligation for 1 and a cis one for 2.


1996 ◽  
Vol 51 (4) ◽  
pp. 531-535 ◽  
Author(s):  
Stefan Anfang ◽  
Kurt Dehnicke ◽  
Jörg Magull

Abstract [DyCl3(DME)2] (DME = 1,2-dimethoxyethane) has been prepared from the known tetrahy-drofuran complex [Dy2Cl6(THF)7] in boiling DME. Both complexes were characterized by structure determinations. [DyCl3(DME)2]: Space group P21/c, Z = 4, lattice dimensions at -70 °C: a = 1141.9(6), b = 884.2(4), c = 1558.3(6) pm, β = 104.83(4)°. The complex has a molecular structure with a distorted pentagonal bipyramidal geometry in which the oxygen atoms of the chelating DME molecules and one chlorine atom occupy the pentagonal plane. [DyCl2(THF)5]+[DyCl4(THF)2]-: Space group C2/c, Z = 4, lattice dimensions at -70 °C: a -1241.4(9), b = 1139.4(6), c = 2735.1(19) pm, β = 91.19(4)°. The complex contains a seven-coordinate cation with axial chloride ligands in a pentagonal bipyramidal structure and a six-coordinate anion with a trans octahedral geometry.


2020 ◽  
Vol 76 (6) ◽  
pp. 562-571 ◽  
Author(s):  
Levi Senior ◽  
Anthony Linden

The crystal structures of six halobismuth(III) salts of variously substituted aminopyridinium cations display discrete mononuclear [BiCl6]3− and dinuclear [Bi2 X 10]4− anions (X = Cl or Br), and polymeric cis-double-halo-bridged [Bi nX 4 n ] n− anionic chains (X = Br or I). Bis(2-amino-3-ammoniopyridinium) hexachloridobismuth(III) chloride monohydrate, (C5H9N3)2[BiCl6]Cl·H2O, (1), contains discrete mononuclear [BiCl6]3− and chloride anions. Tetrakis(2-amino-3-methylpyridinium) di-μ-chlorido-bis[tetrachloridobismuth(III)], (C6H9N2)4[Bi2Cl10], (2), tetrakis(2-amino-3-methylpyridinium) di-μ-bromido-bis[tetrabromidobismuth(III)], (C6H9N2)4[Bi2Br10], (3), and bis(4-amino-3-ammoniopyridinium) di-μ-chlorido-bis[tetrachloridobismuth(III)] dihydrate, (C5H9N3)2[Bi2Cl10]·2H2O, (4), incorporate discrete [Bi2 X 10]4− anions (X = Cl or Br), while catena-poly[2,6-diaminopyridinium [[cis-diiodidobismuth(III)]-di-μ-iodido]], {(C5H8N3)[BiI4]} n , (5), and catena-poly[2,6-diaminopyridinium [[cis-dibromidobismuth(III)]-di-μ-bromido]], {(C5H7N2)[BiBr4]} n , (6), include [Bi nX 4 n ] n− anionic chains (X = Br or I). Structures (2) and (3) are isostructural, while that of (5) is a pseudomerohedral twin. There is no discernible correlation between the type of anionic species obtained and the cation or halide ligand used. The BiIII centres always have a slightly distorted octahedral geometry and there is a correlation between the Bi—X bond lengths and the number of classic N—H...X hydrogen bonds that the X ligand accepts, with a greater number of interactions corresponding with slightly longer Bi—X distances. The supramolecular networks formed by classic N—H...X hydrogen bonds include ladders, bilayers and three-dimensional frameworks.


1999 ◽  
Vol 54 (2) ◽  
pp. 171-178 ◽  
Author(s):  
Mutlaq Al-Jahdali ◽  
Paul K. Baker ◽  
Michael G. B. Drew

Treatment of [Ml2(CO)3(NCMe)2] (M = Mo, W) with two equivalents of EtC2Et in CH2CI2 at 0°C yields the bis(3-hexyne) complexes [MI2(CO)(NCMe)(η2-EtC2Et)2] (1 and 2). Complexes 1 and 2 react with two equivalents of PPh3 in CH2CI2 to give the complexes [Ml2(CO)(PPh3)2 (η2-EtC2Et)] (3 and 4). The molecular structure of 4 (M = W) has been crystallographically determined and has a pseudo-octahedral geometry with the two PPh3 ligands trans to each other with the two cis-iodo-ligands, which together with the carbonyl and 3-hexyne ligand are occupying the equatorial plane. Reaction of 1 and 2 with an equimolar amount of Ph2P(CH2)nPPh2 (for M = Mo, n =1; for M = W, n = 1 to 6 ) in CH2CI2 affords the mono(3-hexyne) complexes [Ml2(CO){Ph2P(CH2)nPPh2}(η2-EtC2Et)] (5 - 11). The tungsten complex [Wl2(CO){Ph2P(CH2)3PPh2}(η2-EtC2Et)] (8 ) has also been crystallographically characterised and has cis-phosphorus atoms in the equatorial plane with the carbonyl and one of the iodo-ligands, with the other iodo-ligand and the 3-hexyne occupying the axial sites.


2009 ◽  
Vol 96 (3) ◽  
pp. 70a-71a ◽  
Author(s):  
Oliver Beckstein ◽  
Elizabeth J. Denning ◽  
Thomas B. Woolf

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