Table 2.

Results of the in-Line Attack of the O_2′ Nucleophile to the Scissile Phosphate from Simulation (Top) and Derived from Crystallographic Structures (Bottom) of Hammerhead Ribozyme^a

simulationb	apo-RS		b-RS		c-RS		c-RS−
R(C17:O2′, C1.1:P)	3.83(19)		3.61(23)		3.55(20)		3.57(16)
angle	138(10)		142(11)		134(14)		140(10)
in-line fitness (F)	0.34(8)		0.43(13)		0.40(10)		0.43(9)
NAC%	0.1		5.6		1.8		2.8
X-ray structuresc	2GOZd	2OEUe	1HMH	1MME	299D	300D	301D	359D
R(C17:O2′, C1.1:P)	3.18	3.30	4.36	4.32	3.46	3.51	4.08	3.54
angle	162.0	152.0	127.0	144.9	56.9	60.0	74.9	63.4
in-line fitness (F)	0.73	0.61	0.20	0.25	0.06	0.07	0.09	0.08

^aShown are the O_2′ · · · P distance, “R(C17:O_2′, C1.1:P)’’, in Å, the O_2′-P–O_5′ angle, “angle’’, in degrees, the in-line fitness parameter, “F’’, defined by Soukup and Breaker,⁵⁷ and the percentage of near-attack conformations, “NAC%’’, defined by Torres and Bruice.²⁸

^bSimulation abbreviations and summaries are given in Table 1.

^cX-ray structures are taken from the Protein Data Bank⁷⁹, ⁸⁰ and labeled by PDB ID.

^dThe full-length hammerhead RNA crystallographic structure at 2.2 Å resolution²⁰ that was also used in this paper as the starting structure.

^eThe full-length hammerhead RNA crystallographic structure at 2.0 Å resolution with resolved Mn²⁺ sites and solvent.²⁴