Structural analysis, by chemical cross-linking with glutardialdehyde (GA), and by urea denaturation, was carried out for the chaperonin oligomer GroEL(14) from Escherichia coli. The crosslinking reaction of GroEL(14) presents two phases: a rapid intralayer cross-linking reaction, which first occurs between the monomers of individual GroEL(7) heptameric rings, and a slow interlayer cross-linking reaction, which later occurs between the two stacked heptameric rings of the GroEL(14) oligomer. The biphasic behavior of the cross-linking reaction indicates that the surfaces of contact between GroEL monomers within individual heptameric rings are more extensive than the surfaces of contact between the two GroEL rings of the oligomer. Millimolar amounts of the divalent cations Mg2+ Mn2+, Ca2+, or Zn2+, but not of monovalent ions, increase the velocity of both intra- and interlayer cross-linking. Divalent cations increase the stability of the native GroEL(14) oligomer in urea. In contrast, Mg2+ activates ATP hydrolysis by GroEL(14), with an activation constant in the micromolar range, while Ca2+ does not significantly assist ATP hydrolysis. It is concluded that divalent cations affect the structure of GroEL(14), in particular the contacts between monomers within the GroEL(7) heptameric layers. The effect of divalent cations on the structure of the chaperonin molecule is quantitatively and qualitatively distinct from that of magnesium ions on the chaperonin ATPase activity.