Anchoring single metal atoms on suitable substrates is a convenient route towards materials with unique electronic and magnetic properties exploitable in a wide range of applications including sensors, data storage, and single atom catalysis (SAC). Among a large portfolio of available substrates, carbon-based materials derived from graphene and its derivatives have received growing concern due to their high affinity to metals combined with biocompatibility, low toxicity, and accessibility. Cyanographene (GCN) as highly functionalized graphene containing homogeneously distributed nitrile groups perpendicular to the surface offers exceptionally favourable arrangement for anchoring metal atoms enabling efficient charge exchange between the metal and the substrate. However, the binding characteristics of metal species can be significantly affected by the coordination effects. Here we employed density functional theory (DFT) calculations to analyse the role of coordination in the binding of late 3d cations (Fe2+, Fe3+, Co2+, Ni2+, Cu2+, Cu+, and Zn2+) to GCN in aqueous solutions. The inspection of several plausible coordination types revealed the most favourable arrangements. Among the studied species, copper cations were found to be the most tightly bonded to GCN, which was also confirmed by the X-ray photoelectron spectroscopy (XPS), atomic absorption spectroscopy (AAS), and isothermal titration calorimetry (ITC) measurements. In general, the inclusion of coordination effects significantly reduced the binding affinities predicted by implicit solvation models. Clearly, to build-up reliable models of SAC architectures in the environments enabling the formation of a coordination sphere, such effects need to be properly taken into account.