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Related Concept Videos

Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
Complexometric Titration: Ligands00:43

Complexometric Titration: Ligands

Different monodentate and polydentate ligands are used as complexing agents in complexometric titration reactions. The formation of complexes by mono- and bidentate ligands involves two or more intermediate steps, limiting their use as complexing agents. In comparison, polydentate ligands can form complexes with metal ions in a single-step process, facilitating sharper end points. This means polydentate ligands, such as amino carboxylic acid derivatives, are most commonly employed in...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Related Experiment Video

Updated: Jun 16, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Assisted assignment of ligands corresponding to unknown electron density.

T Andrew Binkowski1, Marianne Cuff, Boguslaw Nocek

  • 1Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. abinkowski@anl.gov

Journal of Structural and Functional Genomics
|January 22, 2010
PubMed
Summary
This summary is machine-generated.

A new computational method aids in identifying unknown bound ligands by comparing electron density surfaces to a database of known ligand binding sites. This approach helps determine ligand identity in structural biology research.

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Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides
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Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Published on: September 7, 2019

Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biochemistry

Background:

  • Identifying bound ligands from unknown electron density is crucial in structural biology.
  • Current methods can be time-consuming and require expert interpretation.

Purpose of the Study:

  • To develop a semi-automated computational procedure for identifying bound ligands from unknown electron density.
  • To assist crystallographers in assigning ligand identity during structure determination.

Main Methods:

  • Comparing the atomic surface of an unknown electron density blob to a library of 3D ligand binding surfaces from the Protein Data Bank (PDB).
  • Utilizing physicochemical texture and geometric shape similarity assessments for ligand identification.
  • Benchmarking the method against known ligands in the PDB.

Main Results:

  • The method successfully identified correct ligands based on binding surface comparisons in benchmark tests.
  • Demonstrated application in model building and refinement for structural genomics targets with unknown density blobs.
  • Validated against highly observed ligands from the Protein Data Bank.

Conclusions:

  • The developed semi-automated computational method effectively assists in assigning ligand identity to unknown electron density.
  • This tool shows promise for high-throughput structural genomics pipelines.
  • Enhances the efficiency and accuracy of ligand identification in crystallographic studies.