As Adeptus points out, Call Lightning's effect extends in a radius from the targeted point. Per the general rules on spells' area of effect:
A spell's effect expands in straight lines from the point of origin.
As for where that point may be placed, the 2019 Sage Advice Compendium clarifies this matter for a different spell that functions in a similar way on page 14:
Using 5-foot squares, does cloud of daggers affect a single square? Cloud of daggers (5 ft. cube) can affect more than one square on a grid, unless the DM says effects snap to the grid. There are many ways to position that cube.
The point here is that a point (or area of effect) is not required to "snap" to the grid. In the case of Call Lightning, the point may be positioned at the intersection of grid spaces, thereby affecting up to 4 adjacent targets/spaces.
It may also be positioned smack in the middle of a space. In this case, a 5 foot radius technically extends to include the 8 spaces around the centrally targeted grid space.
However, the rule on space states:
A creature's space is the area in feet that it effectively controls in combat, not an expression of its physical dimensions. A typical Medium creature isn't 5 feet wide, for example, but it does control a space that wide.
This means that, even though the 5-foot radius extends into the adjacent 8 spaces, it doesn't necessarily mean that all creatures in those spaces are literally within 5 feet at any given time.
Allowing only a single creature/space to be affected by a lightning strike (as you propose) seems a little underpowered to me while allowing it to affect up to 8 might be pushing the bounds of what is reasonably balanced. Ultimately a DM must adjudicate how to handle each specific situation.
For my money, if four spaces are affected when a grid intersection is targeted, that seems like a good standard maximum to use.