Methyl-coenzyme M reductase (MCR) is the key enzyme in methane formation by methanogenic Archaea. It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B. The catalytic mechanism of MCR and the role of its prosthetic group, the nickel hydrocorphin coenzyme F-430, is still disputed, and no intermediates have, been observed so far by fast spectroscopic techniques when the enzyme was incubated with the natural substrates. In the presence of the competitive inhibitor coenzyme M instead of methyl-coenzyme M, addition of coenzyme B to the active Ni(I) state MCRred1 induces two new species called MCRred2a and MCRred2r which have been characterized by pulse EPR spectroscopy. Here we show that the two MCRred2 signals can also be induced by the S-methyl- and the S-trifluoromethyl analogs of coenzyme B. F-19-ENDOR data for MCRred2a and MCRred2r induced by S-CF3-coenzyme B show that, upon binding of the coenzyme B analog, the end of the 7-thioheptanoyl chain of coenzyme B moves closer to the nickel center of F-430 by more than 2 angstrom as compared to its position in both, the Ni(l) MCRred1 form and the X-ray structure of the inactive Ni(II) MCRox1-silent form. The finding that the protein is able to undergo a conformational change upon binding of the second substrate helps to explain the dramatic change in the coordination environment induced in the transition from MCRred1 to MCRred2 forms and opens the possibility that nickel coordination geometries other than square planar, tetragonal pyramidal, or elongated octahedral might occur in intermediates of the catalytic cycle.