Sentence examples for base in the active from inspiring English sources

If oximes have relatively low pKa values and are deprotonated in the absence of a base in the active site, can these oximes be more nucleophilic than the catalytic serine hydroxyl group to drive the reactivation to completion?

The Ntr domain contains three catalytic aspartates, whereas the PAP domain provides nucleotide specificity through its contact with the base in the active site (Martin & Keller, 2007; Lunde et al, 2012; Munoz-Tello et al, 2012; Yates et al, 2012).

At that point, the side chain of Arg 517 is in a position to form one minor-groove hydrogen bond with the template base in the active site and another with the template base immediately upstream (supplementary Fig 1A online).

These differences might relate to the fact that the ɛ-amino group of the lysine side chain is positioned away from the template, such that it fails to form a hydrogen bond with the template base in the active site, but can form a water-mediated hydrogen bond with the adjacent template base upstream (Fig 2).

This reasoning is in accord with the weak electron densities observed for the arylamine base in the active site of T7 DNA polymerase, where the authors of the previous study also concluded that conformational heterogeneity may hinder the insertion of an incoming nucleotide.

As pointed out above, the evidence for near base-pair resolution derives primarily from the fact that the 19 bp CTCF motif corresponded to fragment end maxima that were 19 bp apart, but also from the close correspondence of the PolII envelope obtained using our method to that obtained using 3'NT, which maps the single 3' base in the active site of PolII.

For example, flipping out the template bases in the active site, a process that has been observed in many polymerases [ 24, 25] may be disturbed in DGR RTs.

The presence of two bases in the active site may allow for the incoming dGTP to pair with the dC present 5′ to the M1dG lesion in the template, thus creating a −1 frameshift product.

The palm and fingers domains interact primarily with the replicative end of the template-primer, wherein the palm (aa 101 109 and 171 338) carries the active site residues (Asp107, Asp198 and Glu199) that catalyze the nucleotidyl transfer reaction, and the fingers domain (aa 110 170) lies over the nascent base pair in the active site formed between 8-oxoG and incoming dATP (described below).

No manganese was added to the reaction, suggesting that the unusual base stacking in the active site does not require the manganese ion bound near the template guanosine.

In contrast, the mismatched dATP stacks above the pyrene ring intercalated in the helix, so that the pyrene mimics a base pair in the active site and facilitates adenine misincorporation by pol ι.