Molybdenum deficiency primarily affects the activity of nitrate reductase, as mentioned in option 4. Nitrate reductase is an enzyme responsible for the conversion of nitrate (NO3-) to nitrite (NO2-) during nitrogen assimilation in plants. Molybdenum is an essential component of this enzyme, and its deficiency can result in reduced nitrate reductase activity.

Option 1 states that molybdenum deficiency affects all the given options, which includes chlorate reductase (option 2) and nitrogenase (option 3) in addition to nitrate reductase. However, this is incorrect. While molybdenum can affect other enzymes in the plant, the primary impact is on nitrate reductase.

Therefore, the correct answer is option 4, which correctly identifies nitrate reductase as the enzyme affected by molybdenum deficiency.