. Author manuscript; available in PMC: 2015 Dec 30.

Published in final edited form as: Chem Res Toxicol. 2005 Mar;18(3):441–456. doi: 10.1021/tx049786v

Table 3.

Composite Evaluation of Structural Distortion in the Dpo4 Ternary Complexes as Compared to Unmodified Control

model	dNTP	HB geometry^a	C1′–C1′ distance^b	Pα–O3′ distance^c	Mg²⁺chelation^d	stacking^e	pocket geomtry^f	protein interaction^g	composite score^h
control intercalation	dTTP	√	√	√	√	√	√	√	0
	dTTP	×	××	×	√	√	×	×	−6
	dCTP	×	××	××	√	××	×	×	−9
	dATP	××	×	×	√	×	×	××	−8
	syn-dATP	×	××	××	√	√	×	×	−7
	dGTP	×	×	×	√	√	×	×	−5
	syn-dGTP	×	×	××	√	√	×	×	−6
major groove type I	dTTP	√	√	×	×	√	√	√	−2
	dCTP	×	×	××	×	√	√	√	−5
	dATP	××	×	××	×	×	√	×	−8
	syn-dATP	×	√	√	×	√	√	×	−3
	dGTP	√	××	××	×	√	√	√	−5
	syn-dGTP	×	√	√	√	√	√	√	−1
–1 deletion	dGTP	√	√	×	√	×	×	××	−5

Coplanarity, distance, angle, occupancy, and number of hydrogen bonds between the nascent base pair are considered. One cross denotes a decrease in one or more of these criteria relative to the control, and the number of hydrogen bonds of >50% occupancy ≥ 1; two crosses denote a decrease in one or more of these criteria and the number of hydrogen bonds of >50% occupancy = 0.

One cross denotes an average value for the C1′–C1′ distance 9.6–10.3 Å or 11.3–12.0 Å; two crosses denote an average value for the C1′–C1′ distance >12.0 or <9.6 Å.

One cross denotes a Pα–O3′ distance occupancy of ≤ 3.6 Å between 1 and 50% of the simulation time; two crosses denote this Pα–O3′ distance occupancy <1%.

Cross denotes disruption of 2–3 of the chelation interactions that involve the two Mg²⁺ ions.

One cross denotes decreased stacking interactions, but some stacking between the nascent base pair and the B[c]Ph moiety or the base pair 3′ to the modified base; two crosses denote no such stacking interactions.

One cross denotes distortion to the dNTP binding pocket geometry, as discussed in the text.

One cross denotes some disruption of hydrogen bonding interactions between the protein residues and the sugar-triphosphate backbone, but the disruption involves no more than three polymerase residues; two crosses denote disruption involving more than three polymerase residues.

Score is based on the unmodified control, which was assigned a base score of 0. Each cross penalizes the base score by –1.