scholarly journals Tools for ligand validation inCoot

2017 ◽  
Vol 73 (3) ◽  
pp. 203-210 ◽  
Author(s):  
Paul Emsley
Keyword(s):  
Model Building ◽  
Ligand Complex ◽  
Molecular Graphics ◽  
X Ray ◽  
Accession Code

Cootis a molecular-graphics program primarily aimed at model building using X-ray data. Recently, tools for the manipulation and representation of ligands have been introduced. Here, these new tools for ligand validation and comparison are described. Ligands in the wwPDB have been scored by density-fit, distortion and atom-clash metrics. The distributions of these scores can be used to assess the relative merits of the particular ligand in the protein–ligand complex of interest by means of `sliders' akin to those now available for each accession code on the wwPDB websites.

scholarly journals Protein–ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation

2017 ◽  
Vol 73 (8) ◽  
pp. 702-709 ◽  
Author(s):  
Hisashi Naitow ◽  
Yoshinori Matsuura ◽  
Kensuke Tono ◽  
Yasumasa Joti ◽  
Takashi Kameshima ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Room Temperature ◽  
Complex Structure ◽  
Binding Mode ◽  
Ligand Complex ◽  
X Ray ◽  
Cell Parameters ◽  
Serial Femtosecond Crystallography ◽  
Small Molecule Ligand

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein–ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.

scholarly journals Synthesis, Crystal Structure, and Fluorescence Properties of Dinuclear and Tetranuclear Zinc(II) Complexes Based on 2-(2’-Hydroxyphenyl)-2-oxazoline

2015 ◽  
Vol 18 (3) ◽  
pp. 155-158 ◽  
Author(s):  
Yuan Zhou ◽  
Qiming Liu ◽  
Yuao Zhang
Keyword(s):  
Crystal Structure ◽  
Fluorescence Emission ◽  
Emission Spectra ◽  
Methanol Solution ◽  
Ligand Complex ◽  
Fluorescence Emission Spectra ◽  
Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Strong Luminescence

Two new zinc(II) complexes have been prepared by reaction of 2-(2’-Hydroxyphenyl)-2-oxazoline(Hoz) with Zn(acac)2 and ZnCl2 respectively. The complexes are characterized by IR and X-ray crystallography. Complex 1 is dinuclear zinc structure bridged by the oxygen atoms from oz- ligand and acac- ligand as terminal chelating ligand. Complex 2 is tetranuclear zinc structure bridged by both μ2-oxygen from oz- ligand and μ3-methoxide. 1 crystalizes in P21 space group with crystallographic parameters: a=9.3842Å19), b=13.5840 Å30), c=11.1380 Å20), β=96.250°(30). 2 crystalizes in P-1 space group with crystallographic parameters: a=9.5517Å(19), b=11.1234Å(22), c=11.1826Å(22), α=102.820°(30), β=114.988°(30), γ=100.806°(30). The UV absorption and fluorescence emission spectra are measured on the methanol solution and solid state of complex 1 and it shows strong luminescence.

Synthesis and Structural Characterization of the Mixed Ligand Complex [Cu(Hml)2(Phen)] · 2 H2O (H2ml = 2-Methyllactic Acid)

2003 ◽  
Vol 58 (1) ◽  
pp. 151-154 ◽  
Author(s):  
Rosa Carballo ◽  
Berta Covelo ◽  
Ezequiel M. Vázquez-Lópeza ◽  
Alfonso Castiñeiras ◽  
Juan Niclós
Keyword(s):  
Magnetic Measurements ◽  
Mixed Ligand Complex ◽  
Three Dimensional ◽  
Mixed Ligand ◽  
Water Molecules ◽  
Ligand Complex ◽  
X Ray ◽  
Dimensional Network ◽  
Distorted Octahedral

Abstract A new mixed-ligand complex of copper(II) with 1,10-phenanthroline and 2-methyllactate was prepared. [Cu(HmL)2(phen)] ·2H2O (where HmL = monodeprotonated 2-methyllactic acid) was characterized by elemental analysis, IR, electronic and EPR spectroscopy, magnetic measurements at room temperature, thermogravimetric analysis and X-ray diffractometry. The copper atom is in a tetragonally distorted octahedral environment and the 2-methyllactato ligand is bidentately chelating. The presence of lattice water molecules mediates the formation of a three-dimensional network.

Using cryo-electron microscopy maps for X-ray structure determination of homologues

2020 ◽  
Vol 76 (1) ◽  
pp. 63-72
Author(s):  
Lingxiao Zeng ◽  
Wei Ding ◽  
Quan Hao
Keyword(s):  
Electron Microscopy ◽  
Hybrid Method ◽  
Model Building ◽  
Test Cases ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sequence Identity ◽  
Whole Process ◽  
Cryo Electron Microscopy

The combination of cryo-electron microscopy (cryo-EM) and X-ray crystallography reflects an important trend in structural biology. In a previously published study, a hybrid method for the determination of X-ray structures using initial phases provided by the corresponding parts of cryo-EM maps was presented. However, if the target structure of X-ray crystallography is not identical but homologous to the corresponding molecular model of the cryo-EM map, then the decrease in the accuracy of the starting phases makes the whole process more difficult. Here, a modified hybrid method is presented to handle such cases. The whole process includes three steps: cryo-EM map replacement, phase extension by NCS averaging and dual-space iterative model building. When the resolution gap between the cryo-EM and X-ray crystallographic data is large and the sequence identity is low, an intermediate stage of model building is necessary. Six test cases have been studied with sequence identity between the corresponding molecules in the cryo-EM and X-ray structures ranging from 34 to 52% and with sequence similarity ranging from 86 to 91%. This hybrid method consistently produced models with reasonable R work and R free values which agree well with the previously determined X-ray structures for all test cases, thus indicating the general applicability of the method for X-ray structure determination of homologues using cryo-EM maps as a starting point.

X-Ray Diffraction and Molecular Model Building Studies of The Interaction of Actinomycin with Nucleic Acids

Nature ◽  
1963 ◽  
Vol 198 (4880) ◽  
pp. 538-540 ◽  
Author(s):  
L. D. HAMILTON ◽  
W. FULLER ◽  
E. REICH
Keyword(s):  
Nucleic Acids ◽  
Model Building ◽  
Molecular Model ◽  
X Ray Diffraction ◽  
X Ray

scholarly journals The dimensions and shapes of the furanose rings in nucleic acids

1972 ◽  
Vol 130 (2) ◽  
pp. 453-465 ◽  
Author(s):  
S. Arnott ◽  
D. W. L. Hukins
Keyword(s):  
Nucleic Acids ◽  
Model Building ◽  
Molecular Model ◽  
Relative Orientation ◽  
Ring Conformation ◽  
Mean Values ◽  
Pyrimidine Base ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ring Puckering

A survey was made of the geometry of furanose rings in β-nucleotides and β-nucleosides (as monomers related to nucleic acids) for which structures have been determined by X-ray crystallography. Mean values, and estimated standard deviations from them, were calculated for bond-lengths, bond-angles and conformation-angles. For parameters with values dependent on ring-puckering, separate calculations were made for each ring type. (The rings are puckered in one of three conformations: C-2- or C-3-endo or C-3-exo; C-2-exo has not been observed.) The results were used to compute standard furanose rings with C-2-endo, C-3-endo and C-3-exo conformations for use in nucleic acid molecular model-building. The survey also showed that the only other conformation-angle in nucleotides dependent on the furanose ring conformation corresponds to the relative orientation of the purine (or pyrimidine) base and the ring.

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