Cobalt-substituted zinc finger 3 of transcription factor IIIA: interactions with cognate DNA detected by (31)P ENDOR spectroscopy

We show the first ENDOR study of the coordination environment of high-spin Co(II) in a biological system with a study of DNA binding to the Co-substituted Cys2/His2 single Zn-finger domain, Finger 3 (F3), from the prototypical zinc finger protein, transcription factor IIIA (TFIIIA) from Xenopus laevis. High covalency to cysteine and histidine is implied by ENDOR-derived 1H couplings to protons of cysteinyl ligands and 14N couplings to histidyl nitrogens, results which support the expectation that Zn(II) and Co(II) bind to F3 in a very similar manner. No changes in either 1H or 14N ENDOR were detected upon binding Co(II)-F3 to C-block DNA. Of particular importance to the use of Co(II) substitution for Zn(II), the ENDOR method shows that Co(II)-F3 undergoes sequence-specific binding to the cognate DNA for Zn(II)-F3, the internal control region (ICR) of the 5S rRNA (C-block). 31P ENDOR measurements yield a Co-31P distance of rCo-P = 8.1(3) A to the nearest backbone phosphodiester of the C-block. Interestingly, a 31P ENDOR doublet observed for Co(II)-F3 in phosphate buffer indicates that inorganic phosphate (Pi) binds at a comparable distance from Co as does the nearest phosphate of DNA, presumably at the same site.