The structural organization of DNA in complex with linker histone H1 and non-histone chromosomal protein HMGB1 in presence of calcium and manganese ions have been studied using FTIR and UV circular dichroism spectroscopy. We have demonstrated that the presence of calcium ions leads to the formation of highly ordered DNA-H1-HMGB1 structures, while manganese ions decrease the order in the earlier reported nanoscale complexes.