Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein−Ligand Complexes

2007 ◽  
Vol 47 (2) ◽  
pp. 668-675 ◽  
Author(s):  
Yipin Lu ◽  
Renxiao Wang ◽  
Chao-Yie Yang ◽  
Shaomeng Wang
Keyword(s):  
High Resolution ◽  
Crystal Structures ◽  
Bound Water ◽  
Water Molecules

scholarly journals Crystal structures of the elusive Rhizobium etli l-asparaginase reveal a peculiar active site

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joanna I. Loch ◽  
Barbara Imiolczyk ◽  
Joanna Sliwiak ◽  
Anna Wantuch ◽  
Magdalena Bejger ◽  
...  
Keyword(s):  
High Resolution ◽  
Crystal Structures ◽  
Active Site ◽  
Chemical Properties ◽  
Bound Water ◽  
Bacterial Symbiont ◽  
Water Molecules ◽  
Rhizobium Etli ◽  
Catalytic Role ◽  
Asparaginase Activity

AbstractRhizobium etli, a nitrogen-fixing bacterial symbiont of legume plants, encodes an essential l-asparaginase (ReAV) with no sequence homology to known enzymes with this activity. High-resolution crystal structures of ReAV show indeed a structurally distinct, dimeric enzyme, with some resemblance to glutaminases and β-lactamases. However, ReAV has no glutaminase or lactamase activity, and at pH 9 its allosteric asparaginase activity is relatively high, with Km for l-Asn at 4.2 mM and kcat of 438 s−1. The active site of ReAV, deduced from structural comparisons and confirmed by mutagenesis experiments, contains a highly specific Zn2+ binding site without a catalytic role. The extensive active site includes residues with unusual chemical properties. There are two Ser-Lys tandems, all connected through a network of H-bonds to the Zn center, and three tightly bound water molecules near Ser48, which clearly indicate the catalytic nucleophile.

Extrem asymmetrisch gebundene Wassermoleküle-Kristallstrukturen von Sr(OH)Cl · 4 H2O, Sr(OH)Br · 4 H2O und Ba(OH)I·4 H2O / Extremely Asymmetrically Bound Water Molecules-Crystal Structures of Sr(OH)Cl · 4 H2O, Sr(OH)Br · 4 H2O, and Ba(OH)I·4 H2O

1991 ◽  
Vol 46 (10) ◽  
pp. 1279-1286 ◽  
Author(s):  
Thomas Kellersohn ◽  
Konrad Beckenkamp ◽  
Heinz Dieter Lutz
Keyword(s):  
Crystal Structures ◽  
Bound Water ◽  
Structure Type ◽  
Water Molecules ◽  
Halide Ions ◽  
Weak Hydrogen Bond ◽  
Scanning Calorimetry ◽  
Unknown Structure ◽  
Stretching Vibrations ◽  
Strong Distortion

The crystal structures of isotypic Sr(OH)Cl ·4 H2O, Sr(OH)Br·4 H2O, and Ba(OH)I·4 H2O are reported. The title compounds crystallize in a hitherto unknown structure type, space group PĪ, Z = 2. The final R values obtained are 0.0261, 0.069, and 0.062, respectively. The coordination of the metal ions is monocapped square antiprismatic with 7 H2O, 1 OH- and 1 halide ion. The halide ions separate metal/water/hydroxide layers. Each of the four crystallographically different water molecules serves as donor for one very strong and one very weak hydrogen bond and, hence, is extremely asymmetrically bound. Owing to this strong distortion, the largest one known so far, the OH stretching vibrations of the H2O molecules are intramolecularly decoupled as shown from vibrational spectra. The enthalpies of dehydration obtained from differential scanning calorimetry are reported.

scholarly journals Automated identification of elemental ions in macromolecular crystal structures

2014 ◽  
Vol 70 (4) ◽  
pp. 1104-1114 ◽  
Author(s):  
Nathaniel Echols ◽  
Nader Morshed ◽  
Pavel V. Afonine ◽  
Airlie J. McCoy ◽  
Mitchell D. Miller ◽  
...  
Keyword(s):  
High Resolution ◽  
Physical Properties ◽  
Crystal Structures ◽  
Model Building ◽  
Atomic Resolution ◽  
Water Molecules ◽  
Anomalous Scattering ◽  
Magnesium Ions ◽  
Automated Identification ◽  
Test Set

Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms inphenix.refinehave been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy,Bfactor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.

scholarly journals Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids

2021 ◽  
Vol 15 (1) ◽  
pp. 7
Author(s):  
Stephen Neidle
Keyword(s):  
Crystal Structures ◽  
Small Molecule ◽  
Drug Targets ◽  
Bound Water ◽  
Water Molecules ◽  
Telomeric Dna ◽  
Naphthalene Diimide ◽  
In Silico Studies ◽  
G Quadruplex

The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-quadruplexes can be suitable drug targets and many small molecules have been identified to date as G-quadruplex binders, some using computer-based design methods and co-crystal structures. The role of bound water molecules in the crystal structures of G-quadruplex-small molecule complexes has been analyzed in this study, focusing on the water arrangements in several G-quadruplex ligand complexes. One is the complex between the tetrasubstituted naphthalene diimide compound MM41 and a human intramolecular telomeric DNA G-quadruplex, and the others are in substituted acridine bimolecular G-quadruplex complexes. Bridging water molecules form most of the hydrogen-bond contacts between ligands and DNA in the parallel G-quadruplex structures examined here. Clusters of structured water molecules play essential roles in mediating between ligand side chain groups/chromophore core and G-quadruplex. These clusters tend to be conserved between complex and native G-quadruplex structures, suggesting that they more generally serve as platforms for ligand binding, and should be taken into account in docking and in silico studies.

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 Fragments D and Double-D from Fibrinogen and Fibrin

1999 ◽  
Vol 82 (08) ◽  
pp. 271-276 ◽  
Author(s):  
Glen Spraggon ◽  
Stephen Everse ◽  
Russell Doolittle
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Crystal Structures ◽  
Structure And Function ◽  
X Ray ◽  
Long Period ◽  
And Function

IntroductionAfter a long period of anticipation,1 the last two years have witnessed the first high-resolution x-ray structures of fragments from fibrinogen and fibrin.2-7 The results confirmed many aspects of fibrinogen structure and function that had previously been inferred from electron microscopy and biochemistry and revealed some unexpected features. Several matters have remained stubbornly unsettled, however, and much more work remains to be done. Here, we review several of the most significant findings that have accompanied the new x-ray structures and discuss some of the problems of the fibrinogen-fibrin conversion that remain unresolved. * Abbreviations: GPR—Gly-Pro-Arg-derivatives; GPRPam—Gly-Pro-Arg-Pro-amide; GHRPam—Gly-His-Arg-Pro-amide

scholarly journals SANS quantification of bound water in water-soluble polymers across multiple concentration regimes

Soft Matter ◽  
2021 ◽  
Author(s):  
Helen Yao ◽  
Bradley D. Olsen
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Bound Water ◽  
Water Soluble ◽  
Wide Concentration Range ◽  
Water Molecules ◽  
Water Soluble Polymers ◽  
Soluble Polymers

Small-angle neutron scattering is used to measure the number of bound water molecules associating with three polymers over a wide concentration range. Different fitting workflows are evaluated and recommended depending on the concentration regime.

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