Prediction of transition metal-binding sites from apo protein structures

2007 ◽  
Vol 70 (1) ◽  
pp. 208-217 ◽  
Author(s):  
Mariana Babor ◽  
Sergey Gerzon ◽  
Barak Raveh ◽  
Vladimir Sobolev ◽  
Marvin Edelman
Keyword(s):  
Transition Metal ◽  
Metal Binding ◽  
Binding Sites ◽  
Protein Structures ◽  
Metal Binding Sites

Transition-metal binding sites and ligand parameters

1980 ◽  
pp. 2032 ◽  
Author(s):  
Joseph Chatt ◽  
C. T. Kan ◽  
G. Jeffery Leigh ◽  
Christopher J. Pickett ◽  
David R. Stanley
Keyword(s):  
Transition Metal ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Binding Sites ◽  
Ligand Parameters

scholarly journals Check your metal - not every density blob is a water molecule

2014 ◽  
Vol 70 (a1) ◽  
pp. C1483-C1483
Author(s):  
Heping Zheng ◽  
Mahendra Chordia ◽  
David Cooper ◽  
Ivan Shabalin ◽  
Maksymilian Chruszcz ◽  
...  
Keyword(s):  
Coordination Chemistry ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Protein Structures ◽  
Data Bank ◽  
Careful Examination ◽  
Biological Macromolecules ◽  
Metal Binding Sites ◽  
Heterogeneous Chemical

Metals play vital roles in both the mechanism and architecture of biological macromolecules, and are the most frequently encountered ligands (i.e. non-solvent heterogeneous chemical atoms) in the determination of macromolecular crystal structures. However, metal coordinating environments in protein structures are not always easy to check in routine validation procedures, resulting in an abundance of misidentified and/or suboptimally modeled metal ions in the Protein Data Bank (PDB). We present a solution to identify these problems in three distinct yet related aspects: (1) coordination chemistry; (2) agreement of experimental B-factors and occupancy; and (3) the composition and motif of the metal binding environment. Due to additional strain introduced by macromolecular backbones, the patterns of coordination of metal binding sites in metal-containing macromolecules are more complex and diverse than those found in inorganic or organometallic chemistry. These complications make a comprehensive library of "permitted" coordination chemistry in protein structures less feasible, and the usage of global parameters such as the bond valence method more practical, in the determination and validation of metal binding environments. Although they are relatively infrequent, there are also cases where the experimental B-factor or occupancy of a metal ion suggests careful examination. We have developed a web-based tool called CheckMyMetal [1](http://csgid.org/csgid/metal_sites/) for the quick validation of metal binding sites. Moreover, the acquired knowledge of the composition and spatial arrangement (motif) of the coordinating atoms around the metal ion may also help in the modeling of metal binding sites in macromolecular structures. All of the studies described herein were performed using the NEIGHBORHOOD SQL database [2], which connects information about all modeled non-solvent heterogeneous chemical motifs in PDB structure by vectors describing all contacts to neighboring residues and atoms. NEIGHBORHOOD has broad applications for the validation and data mining of ligand binding environments in the PDB.

scholarly journals Metal-binding sites of concanavalin A and their role in the binding of α-methyl d-glucopyranoside

1968 ◽  
Vol 109 (4) ◽  
pp. 669-672 ◽  
Author(s):  
A. Joseph Kalb ◽  
Alexander Levitzki
Keyword(s):  
Transition Metal ◽  
Concanavalin A ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Ion Binding ◽  
Transition Metal Ion ◽  
Metal Binding Sites ◽  
Ion Binding Sites

Binding of a transition metal ion to specific sites in concanavalin A induces the formation of specific Ca2+ ion-binding sites. Sites for binding α-methyl d-glucopyranoside exist only when a transition metal ion and Ca2+ ion are bound.

scholarly journals Transition metal ion FRET to measure short-range distances at the intracellular surface of the plasma membrane

2016 ◽  
Vol 147 (2) ◽  
pp. 189-200 ◽  
Author(s):  
Sharona E. Gordon ◽  
Eric N. Senning ◽  
Teresa K. Aman ◽  
William N. Zagotta
Keyword(s):  
Plasma Membrane ◽  
Transition Metal ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Head Group ◽  
Transition Metal Ion ◽  
Metal Binding Sites

Biological membranes are complex assemblies of lipids and proteins that serve as platforms for cell signaling. We have developed a novel method for measuring the structure and dynamics of the membrane based on fluorescence resonance energy transfer (FRET). The method marries four technologies: (1) unroofing cells to isolate and access the cytoplasmic leaflet of the plasma membrane; (2) patch-clamp fluorometry (PCF) to measure currents and fluorescence simultaneously from a membrane patch; (3) a synthetic lipid with a metal-chelating head group to decorate the membrane with metal-binding sites; and (4) transition metal ion FRET (tmFRET) to measure short distances between a fluorescent probe and a transition metal ion on the membrane. We applied this method to measure the density and affinity of native and introduced metal-binding sites in the membrane. These experiments pave the way for measuring structural rearrangements of membrane proteins relative to the membrane.

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