Although involved in various physiological functions, nucleoside bis-phosphate analogues and their metal-ion complexes have been scarcely studied. Hence, here, we explored the solution conformation of 2′-deoxyadenosine- and 2′-deoxyguanosine-3′,5′-bisphosphates, 3 and 4, d(pNp), as well as their Zn²⁺/Mg²⁺ binding sites and binding-modes (i.e. inner- vs. outer-sphere coordination), acidity constants, stability constants of their Zn²⁺/Mg²⁺ complexes, and their species distribution. Analogues 3 and 4, in solution, adopted a predominant Southern ribose conformer (ca. 84%), gg conformation around C4′–C5′ and C5′–O5′ bonds, and glycosidic angle in the anti-region (213–270°). ¹H- and ³¹P-NMR experiments indicated that Zn²⁺/Mg²⁺ ions coordinated to P5′ and P3′ groups of 3 and 4 but not to N7 nitrogen atom. Analogues 3 and 4 formed ca. 100-fold more stable complexes with Zn²⁺vs. Mg²⁺-ions. Complexes of 3 and 4 with Mg²⁺ at physiological pH were formed in minute amounts (11% and 8%, respectively) vs. Zn²⁺ complexes (46% and 44%). Stability constants of Zn²⁺/Mg²⁺ complexes of analogues 3 and 4 (log K^M_ML = 4.65–4.75/2.63–2.79, respectively) were similar to those of the corresponding complexes of ADP and GDP (log K^M_ML = 4.72–5.10/2.95–3.16, respectively). Based on the above findings, we hypothesized that the unexpectedly low log K values of Zn²⁺-d(pNp) as compared to Zn²⁺-NDP complexes, are possibly due to formation of outer-sphere coordination in the Zn²⁺-d(pNp) complex vs. inner-sphere in the NDP-Zn²⁺ complex, in addition to loss of chelation to N7 nitrogen atom in Zn²⁺-d(pNp). Indeed, explicit solvent molecular dynamics simulations of 1 and 3 for 100 ns supported this hypothesis.