scholarly journals Water spines and networks in G-quadruplex structures

2020 ◽  
Author(s):  
Kevin Li ◽  
Liliya Yatsunyk ◽  
Stephen Neidle
Keyword(s):  
Hydrogen Bond ◽  
High Resolution ◽  
Water Molecule ◽  
Crystal Structures ◽  
Water Molecules ◽  
Nmr Structures ◽  
Loop Conformations ◽  
G Quadruplex ◽  
Guanine Base ◽  
Loop Regions

Abstract Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.

Crystal structures of nickel(II) and copper(Il)-Schiff-bases complexes with tetramic and tetronic acid subunits

1994 ◽  
Vol 209 (12) ◽  
Author(s):  
G. Reck ◽  
B. Schulz ◽  
A. Zschunke ◽  
O. Tietze ◽  
J. Haferkorn
Keyword(s):  
Complex Formation ◽  
Water Molecule ◽  
Crystal Structures ◽  
Schiff Bases ◽  
Water Molecules ◽  
Ligand Molecule ◽  
Tetragonal Pyramid ◽  
Space Group ◽  
Tetronic Acid ◽  
Oxygen Ligand

AbstractN,N′-ethylene-bis-(tetronic-acid-3-formiminato)-copper(II)/K1 crystallizes in space groupN,N′-ethylene-bis-(tetronic-acid-3-formiminato)-nikkel(II)/K2 crystallizes in space groupN,N′-ethylene-bis-(1,5,5-trimethyltetramic-acid-3-formiminato)-copper(II)/K3 crystallizes in space groupIn K1 and K3 copper is coordinated by two nitrogen and two oxygen atoms of the ligand molecule as well as by one water molecule on top of a tetragonal pyramid. In K2 two water molecules are included in the complex formation. These and two nitrogen as well as two oxygen ligand atoms form a nearly regular octahedron.

scholarly journals 2,2′-Bipyridin-1-ium hemioxalate oxalic acid monohydrate

IUCrData ◽  
2018 ◽  
Vol 3 (8) ◽  
Author(s):  
Błażej Dziuk ◽  
Anna Jezuita
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Oxalic Acid ◽  
Water Molecule ◽  
Title Compound ◽  
Water Molecules ◽  
Asymmetric Unit ◽  
Compound C ◽  
Oxalic Acids

The asymmetric unit of the title compound, C10H9N2 +·0.5C2O4 2−·C2H2O4·H2O, consists of a 2,2′-bipyridinium cation, half an oxalate dianion, one oxalic acid and one water molecule. One N atom in 2,2′-bipyridine is unprotonated, while the second is protonated and forms an N—H...O hydrogen bond. In the crystal, the anions are connected with surrounding acid molecules and water molecules by strong near-linear O—H...O hydrogen bonds. The water molecules are located between the anions and oxalic acids; their O atoms participate as donors and acceptors, respectively, in O—H...O hydrogen bonds, which form sheets arranged parallel to the ac plane.

Prediction of Interaction of Citric Acid Modified Cellulose with Water Region Using Molecular Modelling Technique

2019 ◽  
Vol 797 ◽  
pp. 118-126
Author(s):  
Nornizar Anuar ◽  
Wan Nor Asyikin Wan Mohamed Daid ◽  
Sopiah Ambong Khalid ◽  
Sarifah Fauziah Syed Draman ◽  
Siti Rozaimah Sheikh Abdullah
Keyword(s):  
Hydrogen Bond ◽  
Citric Acid ◽  
Water Molecule ◽  
Hydration Shell ◽  
Computational Technique ◽  
Water Molecules ◽  
Ferric Ion ◽  
Water Loading ◽  
Higher Temperature ◽  
Modified Cellulose

In this paper, chemically modified cellulose was used instead of cellulose as it offers higher adsorption capacities, great chemical strength and good resistance to heat. As part of Phyto-Adsorption Remediation Method, citric acid modified cellulose (CAMC) was used to treat ferric ion. However, there is a large possibility that CAMC molecule might interact with water molecule that contain hydrogen bond and hence pose as a competitor to ferric acid and reduces the efficiency of CAMC in ferric ion removal. Thus, the aim of this work is to identify the most stable hydrogen bond between CAMC and water, by using a computational technique. The interaction between the water molecules and CAMC was observed by varying the volume of water molecule with modified cellulose by an expansion in amorphous region. The simulation result shows that for water loading less than 20 molecules, the interaction between water molecules and CAMC is higher at temperature 311K, whilst for water loading higher than 20 molecules, the interaction weakens at higher temperature. This work proves that water molecules have the tendency to bind to carboxyl group of glucose, to oxygen of ester and to oxygen of anhydride acid of the CAMC molecule, which might pose a competition for ferric acid removal. The calculation of coordination number has shown that the number of atoms present in the first hydration shell (of radius < 2.5Å) is more as the temperature increases from 298K to 311K, which indicates that the adsorption is better at higher temperature. For hydration shell at radius >2.5Å, cell temperature is not significant to the number of atoms present.

scholarly journals 2-(3-{(3R,4R)-4-Methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}oxetan-3-yl)acetonitrile monohydrate

2014 ◽  
Vol 70 (4) ◽  
pp. o382-o383
Author(s):  
Matthias Gehringer ◽  
Ellen Pfaffenrot ◽  
Peter R. W. E. F. Keck ◽  
Dieter Schollmeyer ◽  
Stefan A. Laufer
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Organic Molecules ◽  
Crystal Packing ◽  
Intermolecular Hydrogen Bond ◽  
Chair Conformation ◽  
Pyrimidine Ring ◽  
Piperidine Ring ◽  
Water Molecules ◽  
Compound C

In the title compound, C18H24N6O·H2O, the piperidine ring adopts a chair conformation with an N—C—C—C torsion angle of 39.5 (5)° between thecis-related substituents. The pyrrole N—H group forms a water-mediated intermolecular hydrogen bond to one of the N atoms of the annelated pyrimidine ring. The water molecule connects two organic molecules and is disorderd over two positions (occupancies of 0.48 and 0.52). The crystal packing shows zigzag chains of alternating organic and water molecules running parallel to theaaxis.

scholarly journals Crystal Structures of the Ferrous Dioxygen Complex of Wild-type Cytochrome P450eryF and Its Mutants, A245S and A245T

2005 ◽  
Vol 280 (23) ◽  
pp. 22102-22107 ◽  
Author(s):  
Shingo Nagano ◽  
Jill R. Cupp-Vickery ◽  
Thomas L. Poulos
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Crystal Structures ◽  
Proton Donor ◽  
Initial Structure ◽  
Hydrogen Bond Network ◽  
Wild Type ◽  
In The Wild ◽  
Site Water ◽  
Bond Network

Cytochrome P450eryF (CYP107A) from Saccaropolyspora ertherea catalyzes the hydroxylation of 6-deoxyerythronolide B, one of the early steps in the biosynthesis of erythromycin. P450eryF has an alanine rather than the conserved threonine that participates in the activation of dioxygen (O2) in most other P450s. The initial structure of P450eryF (Cupp-Vickery, J. R., Han, O., Hutchinson, C. R., and Poulos, T. L. (1996) Nat. Struct. Biol. 3, 632–637) suggests that the substrate 5-OH replaces the missing threonine OH group and holds a key active site water molecule in position to donate protons to the iron-linked dioxygen, a critical step for the monooxygenase reaction. To probe the proton delivery system in P450eryF, we have solved crystal structures of ferrous wild-type and mutant (Fe2+) dioxygen-bound complexes. The catalytic water molecule that was postulated to provide protons to dioxygen is absent, although the substrate 5-OH group donates a hydrogen bond to the iron-linked dioxygen. The hydrogen bond network observed in the wild-type ferrous dioxygen complex, water 63-Glu360-Ser246-water 53-Ala241 carbonyl in the I-helix cleft, is proposed as the proton transfer pathway. Consistent with this view, the hydrogen bond network in the O2·A245S and O2 ·A245T mutants, which have decreased or no enzyme activity, was perturbed or disrupted, respectively. The mutant Thr245 side chain also perturbs the hydrogen bond between the substrate 5-OH and dioxygen ligand. Contrary to the previously proposed mechanism, these results support the direct involvement of the substrate in O2 activation but raise questions on the role water plays as a direct proton donor to the iron-linked dioxygen.

scholarly journals (E)-4-Methoxy-N′-[(6-methyl-4-oxo-4H-chromen-3-yl)methylidene]benzohydrazide monohydrate

2014 ◽  
Vol 70 (7) ◽  
pp. o784-o784 ◽  
Author(s):  
Yoshinobu Ishikawa ◽  
Kohzoh Watanabe
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Benzene Ring ◽  
Dihedral Angle ◽  
Dihedral Angles ◽  
Water Molecules ◽  
Stacking Interactions ◽  
Solvent Water ◽  
Centroid Distance

In the title hydrate, C19H16N2O4·H2O, the 4H-chromen-4-one segment is slightly twisted, with a dihedral angle between the two six-membered rings of 3.30 (5)°. The dihedral angles between the plane of the pyranone ring and the hydrazide plane and between the planes of the pyranone ring and the benzene ring of thep-methoxybenzene unit are 26.69 (4) and 2.23 (3)°, respectively. The molecule is connected to the solvent water molecule by an N—H...O hydrogen bond. In the crystal, there are π–π stacking interactions between centrosymmetrically related pyranone rings [centroid–centroid distance = 3.5394 (9) Å], as well as bridges formed by the water moleculesviaO—H...O hydrogen bonds.

scholarly journals Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes

2020 ◽  
Author(s):  
Karolina Michalska ◽  
Youngchang Kim ◽  
Robert Jedrzejczak ◽  
Natalia I. Maltseva ◽  
Lucy Stols ◽  
...  
Keyword(s):  
Immune Response ◽  
High Resolution ◽  
Water Molecule ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Molecular Targets ◽  
Nonstructural Proteins ◽  
Phosphatase Domain ◽  
Ethanesulfonic Acid ◽  
Precise Role

ABSTRACTAmong 15 nonstructural proteins (Nsps), the newly emerging SARS-CoV-2 encodes a large, multidomain Nsp3. One of its units is ADP-ribose phosphatase domain (ADRP, also known as macrodomain) which is believed to interfere with the host immune response. Such a function appears to be linked to the protein’s ability to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remains unknown. Here, we have determined five, high resolution (1.07 - 2.01 Å) crystal structures corresponding to the apo form of the protein and complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADPr. We show that the protein undergoes conformational changes to adapt to the ligand in a manner previously observed before for in close homologs from other viruses. We also identify a conserved water molecule that may participate in hydrolysis. This work builds foundations for future structure-based research of the ADRP, including search for potential antiviral therapeutics.

scholarly journals (S,Z)-3-Phenyl-2-[(1,1,1-trichloro-7-methoxy-2,7-dioxohept-3-en-4-yl)amino]propanoic acid monohydrate

2014 ◽  
Vol 70 (2) ◽  
pp. o169-o170
Author(s):  
Alex Fabiani Claro Flores ◽  
Juliano Rosa de Menezes Vicenti ◽  
Lucas Pizzuti ◽  
Patrick Teixeira Campos
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Organic Molecule ◽  
Organic Molecules ◽  
Propanoic Acid ◽  
Water Molecules ◽  
Solvent Water ◽  
Compound C

In the title compound, C17H18Cl3NO5·H2O, intramolecular N—H...O and C—H...Cl hydrogen bonds formS(6) andS(5) ring motifs, respectively. The chiral organic molecule is connected to the solvent water molecule by a short O—H...O hydrogen bond. In the crystal, a weak C—H...Cl interaction connects the organic molecules along [100] while the water molecules act as bridges between the organic molecules in both the [100] and [010] directions, generating layers parallel to theabplane.

scholarly journals Crystal structures and hydrogen bond analysis of five amino acid conjugates of terephthalic and benzene-1,2,3-tricarboxylic acids

CrystEngComm ◽  
2014 ◽  
Vol 16 (35) ◽  
pp. 8243-8251 ◽  
Author(s):  
Anirban Karmakar ◽  
Clive L. Oliver ◽  
Ana E. Platero-Prats ◽  
Elina Laurila ◽  
Lars Öhrström
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Crystal Structures ◽  
Hirshfeld Surface ◽  
Water Molecules ◽  
Narrow Channels ◽  
Amino Acid Conjugates ◽  
Graph Set ◽  
Hydrogen Bond Analysis ◽  
Hydrogen Bonded

This amino acid derived (red&blue) π-stacked (green) hydrogen bonded (striped) dimer forms a pcu-net with water molecules in the narrow channels. Four related molecules are also presented and all were subjected to graph set and Hirshfeld surface analyses.

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