Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 53

Table 2.6 Coordination patterns of Mg 2þ and Na þ in active site
Cluster NMg 2þ >< CNMg 2þ >< NBMg 2þ >< NNa þ >< CNNa þ >< NBNa þ > Percentage R

u <

RT-C-Mg A 20.78 3.3 144.05 1 1 0 0.05 1 0

B 79.22 4.13 122.66 1 1 0 0.03 1 0

RT-B-Mg A 99.54 3.27 151.1 1 2 1 0 1 0

B 0.46 4 129.76 1 2 1 0.09 1 0

RT-Na A 86.72 3.23 152.91 - - - 1.15 1.99 0.88

B 13.28 4.12 122.82 - - - 1.38 1.54 0.66

dRT-Mg A 100 3.64 154.89 1 2 1 0.97 1.01 0.01

dRT-Na A 23.99 3.5 144.72 - - - 2.96 2.29 2.68

B 76.01 4.3 115.16 - - - 2.46 1.69 1.36

Distances and angles are in ˚ and degrees, respectively. The average values, denoted as <> , are obtained by averaging all snapshots in the cluster. R is the in-line attack
distance (C17:O2 0 to C1.1:P); y is the in-line attack angle (between C17:O2 0 , C1.1:P, and C1.1:O5 0 ); N is the number of ions with at least one coordination to any one of
the four coordination sites; CN is the total coordination number of all ions with at least one coordination to any one of the four coordination sites; NB is the number of
ions which coordinate to at least two of the four coordination sites.