Thanks for the reply Mr. Sundarajan. Can you please elaborate your answer, what cation you are referring having nitrogen? (or even in other cases except proton). In fact, Triphoshates are anions not cations.
N+ in has ammonium ion (cation) is Biologically important for many amino acid metabolic intermediate; in synthesis of excretory product (fish and aquatic invertebrates); in urea cycle by arginine; has Nitric oxide (NO) in vasodilation; neurotransmitor etc
Linear polyamines, like putrescine, spermine and spermidine are also quite important for cellular functions. They bind to DNA and if their synthesis is inhibited, this results in complete stop, or at least severe retardation of cell proliferation. Polyamines are also important modulators of a variety of ion channels, including NMDA receptors and AMPA receptors. Additionally, they play a role in ribosomal frameshifting and can enhance the permeability of the blood-brain barrier.
Why do you want to know? And what do you consider "important". As for connectivity, the proton and NAD+ are among the most connected metabolites. NADP+ and FAD+ are important oxidants. Basic amino-acids are important in protein folding and protein interactions.
It is Sodium, Potassium and Magnesium ion mainly. Sodium Potassium ions are responsible for maintaining the potential difference across the cell membrane which controls the cell wall's permittivity. You can have an idea about this two ion in any bioinorganic book under the heading Sodium-Potassium ion pump. And Magnesium is mainly responsible for ATP hydrolysis and a key element of chlorophyll.
Thanks Soni for correcting me. Yes indeed it was a mistake that I do not follow the question properly. Among the nonmetals B and Al, in minute amount, play a significant role in human body. Al involved in the action of enzymes such as succinic dehydrogenase and d-aminolevulinate dehydrase (involved in porphyrin synthesis). It is believed that boron improves the natural ability of human body to absorb calcium and magnesium. This element is also necessary to allow the brain to function properly. In fact, boron can increase mental alertness.
Apart from NH4+ and H+ that are relevant in human biology, all other non-metal cations are derivatives of the NH4+ that occur as organic molecules like in amino acids, proteins etc. If there are any others, they must be very rare.
Any amino-function (H2N-R) can be protonated forming a cation H3N(+)-R. As mentioned by Edward Sandy, amino acids or proteins are very abundant and many of the amino functions in these molecules are protonated and can thus serve as cations. To tell the full truth: an amino acid H2N-CR2-COOH under normal pH conditions will be in part present as zwitter ion: H3N(+)-CR2-COO(-) only under very acidic conditions (which are not very relevant for real biological systems) amino acids will be protonated: NH3(+)-CR2-COOH. However, already the zwitter ionic forms provide a huge amount of cations (and anions at the same time - of course).
The role of these cations lies mainly in the formation of H-bonds and thus contributing to the structure of enzymes (which determines their function!)
Just to amplify what Axel, Edward, and Igor said, in terms of PREVALENCE the protonated proteins, peptides (GSH), and amino acids, choline and phosphatidylcholine are among the most abundant--ammonia itself isn't very abundant if you're healthy.