Table 2

Metal ion coordination

CationBaseRNA ligandDistance, ÅWater moleculesAverage distance, Å
Mg29G1O1B*2.0W30, W31, W32, W332.1
G2O1P2.0
Mg34G1b#O62.1W35a, W36, W37a, W37b2.1
G19O2P2.1
Mg38§W39, W40, W41, W42, W43, W442.1
Mg45§W46, W47b, W48b, W49, W50, W512.1
Mg52§W53, W54, W55, W56b, W57, W582.1
Mg59G1O3G2.3W35b, W36#, W602.0
G1O2B1.8
G1a#O62.2
Na61G16O2′2.9W922.7
G16N32.8
A21O2P2.7
A21N73.1
Na62C3O2′2.7W1042.8
C3O22.7
G18#O2P2.7
Na63C5O2′2.6W792.9
G6O4′3.1
A21O1P2.7
K64G1O2′3.0W65, W66, W102, W102#2.9
G2N73.1
G2O2P2.7
  • * The letters A, B, and G refer to the α-, β-, and γ-phosphates, respectively, of G1. 

  • The letters a and b refer to alternative positions of nucleotides and water molecules exhibiting disorder. 

  • Symmetry related nucleotides or water molecules are marked by #. 

  • § Coordination shown in Fig. 3

  • Occupancy = 0.5; a dyad dissects the K+—W65 bond and W66 is located on the dyad.