Picometer Resolution Structure of the Coordination Sphere in the Metal-Binding Site in a Metalloprotein by NMR

2020 ◽  
Vol 142 (39) ◽  
pp. 16757-16765
Author(s):  
Andrea Bertarello ◽  
Ladislav Benda ◽  
Kevin J. Sanders ◽  
Andrew J. Pell ◽  
Michael J. Knight ◽  
...  
Keyword(s):  
Binding Site ◽  
Coordination Sphere ◽  
Metal Binding ◽  
Metal Binding Site ◽  
Resolution Structure

scholarly journals Hybrid QM/MM Simulations Confirm Zn(II) Coordination Sphere That Includes Four Cysteines from the P2 × 4R Head Domain

2021 ◽  
Vol 22 (14) ◽  
pp. 7288
Author(s):  
Francisco Andrés Peralta ◽  
J. Pablo Huidobro-Toro ◽  
Raúl Mera-Adasme
Keyword(s):  
Binding Site ◽  
Coordination Sphere ◽  
Metal Binding ◽  
Metal Ion ◽  
Dynamic Simulations ◽  
Metal Binding Site ◽  
Head Domain ◽  
Water Ligands ◽  
Role Of Zn

To ascertain the role of Zn(II) as an allosteric modulator on P2X4R, QM/MM molecular dynamic simulations were performed on the WT and two P2X4R mutants suggested by previous electrophysiological data to affect Zn(II) binding. The Gibbs free energy for the reduction of the putative P2X4R Zn(II) binding site by glutathione was estimated at −22 kcal/mol. Simulations of the WT P2X4R head domain revealed a flexible coordination sphere dominated by an octahedral geometry encompassing C126, N127, C132, C149, C159 and a water molecule. The C132A mutation disrupted the metal binding site, leading to a coordination sphere with a majority of water ligands, and a displacement of the metal ion towards the solvent. The C132A/C159A mutant exhibited a tendency towards WT-like stability by incorporating the R148 backbone to the coordination sphere. Thus, the computational findings agree with previous experimental data showing Zn(II) modulation for the WT and C132A/C159A variants, but not for the C132A mutant. The results provide molecular insights into the nature of the Zn(II) modulation in P2X4R, and the effect of the C132A and C132A/C159A mutations, accounting for an elusive modulation mechanism possibly occurring in other extracellular or membrane protein.

Unraveling the Substrate−Metal Binding Site of Ferrochelatase:  An X-ray Absorption Spectroscopic Study†

Biochemistry ◽  
2002 ◽  
Vol 41 (15) ◽  
pp. 4809-4818 ◽  
Author(s):  
Gloria C. Ferreira ◽  
Ricardo Franco ◽  
Arianna Mangravita ◽  
Graham N. George
Keyword(s):  
Spectroscopic Study ◽  
Binding Site ◽  
Metal Binding ◽  
Metal Binding Site ◽  
X Ray ◽  
Substrate Metal ◽  
X Ray Absorption

scholarly journals Identification and partial characterization of a low affinity metal-binding site in the light chain of tetanus toxin.

1992 ◽  
Vol 267 (13) ◽  
pp. 9053-9058
Author(s):  
J.F. Wright ◽  
M Pernollet ◽  
A Reboul ◽  
C Aude ◽  
M.G. Colomb
Keyword(s):  
Binding Site ◽  
Light Chain ◽  
Metal Binding ◽  
Tetanus Toxin ◽  
Partial Characterization ◽  
Metal Binding Site

Construction of an additional metal-binding site in human metallothionein-2

2006 ◽  
Vol 101 (4) ◽  
pp. 354-360 ◽  
Author(s):  
Mitsutoshi Toyama ◽  
Mariko Sasaki ◽  
Noriaki Hirayama ◽  
Yoshikatsu Murooka ◽  
Mitsuo Yamashita
Keyword(s):  
Binding Site ◽  
Metal Binding ◽  
Metal Binding Site
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