Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

ChemBioChem ◽  
2019 ◽  
Vol 21 (4) ◽  
pp. 517-522 ◽  
Author(s):  
Tatsuya Funai ◽  
Megumi Aotani ◽  
Risa Kiriu ◽  
Junko Nakamura ◽  
Yuki Miyazaki ◽  
...  
Keyword(s):  
Metal Ion ◽  
Dna Polymerases ◽  
Base Pairs ◽  
Ion Specificity

scholarly journals Crystal structure of d(CCGGGGTACCCCGG)2at 1.4 Å resolution

2017 ◽  
Vol 73 (5) ◽  
pp. 259-265
Author(s):  
Selvam Karthik ◽  
Arunachalam Thirugnanasambandam ◽  
Pradeep Kumar Mandal ◽  
Namasivayam Gautham
Keyword(s):  
Crystal Structure ◽  
Metal Ion ◽  
Double Helix ◽  
Barium Chloride ◽  
Base Pairs ◽  
X Ray ◽  
Density Map ◽  
Solvent Molecules ◽  
Electron Density Map ◽  
Phosphate Groups

The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2is reported at 1.4 Å resolution in the tetragonal space groupP41212. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the backbone phosphate groups.

scholarly journals Mutation of outer-shell residues modulates metal ion co-ordination strength in a metalloenzyme

2010 ◽  
Vol 429 (2) ◽  
pp. 313-321 ◽  
Author(s):  
Jee-Loon Foo ◽  
Colin J. Jackson ◽  
Paul D. Carr ◽  
Hye-Kyung Kim ◽  
Gerhard Schenk ◽  
...  
Keyword(s):  
Metal Ion ◽  
Structural Data ◽  
Biochemical Properties ◽  
Outer Shell ◽  
Model Systems ◽  
Spectroscopic Techniques ◽  
Structural Determinants ◽  
Ion Specificity ◽  
X Ray Crystallography ◽  
Metal Ion Interactions

The metal ion co-ordination sites of many metalloproteins have been characterized by a variety of spectroscopic techniques and small-molecule model systems, revealing many important insights into the structural determinants of metal ion co-ordination. However, our understanding of this fundamentally and practically important phenomenon remains frustratingly simplistic; in many proteins it is essentially impossible to predict metal ion specificity and the effects of remote ‘outer-shell’ residues on metal ion co-ordination strength are also poorly defined. This is exemplified by our inability to explain why metalloenzymes with identical metal ion co-ordination spheres, such as the closely related orthologues of bacterial PTE (phosphotriesterase) from Agrobacterium radiobacter and Pseudomonas diminuta, display different metal ion specificity and co-ordination strength. In the present study, we present a series of PTE variants that all possess identical metal ion co-ordination spheres, yet display large differences in their metal ion co-ordination strength. Using measurement of the rates of metal ion dissociation from the active site alongside analysis of structural data obtained through X-ray crystallography, we show that ‘outer-shell’ residues provide essential support for the metal ion ligands, in effect buttressing them in their optimal orientation. Remote mutations appear to modulate metal ion interactions by increasing or decreasing the stabilizing effects of these networks. The present study therefore provides a description of how the greater protein fold can be modified to ‘tune’ the strength of metal ion co-ordination and metal ion specificity, as well as reinforcing the concept of proteins as ensembles of conformational states with unique structures and biochemical properties.

Metal ion specificity in the oxidation of the coordinated mercapto group

1978 ◽  
Vol 17 (7) ◽  
pp. 2037-2039 ◽  
Author(s):  
Paul R. Butler ◽  
Elliott L. Blinn
Keyword(s):  
Metal Ion ◽  
Mercapto Group ◽  
Ion Specificity
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