Is there any way to fix this?
It's too late to do anything but filter out the noise. The sky is easy; you just mask it and run a median filter on it. The detailed areas, however, will get softer if you filter the noise.
Other than say "check the settings before you use the camera", I would also suggest that you learn to "expose to the right". Check your histogram after a shot like that; the clouds should be almost touching the right edge in JPEG, or start clipping a little if you're shooting in RAW and using a converter that is good at preserving highlights. I see you used a gamma of +1.4 in post-processing. This indicates under-exposure in the camera.
I haven't studied noise characteristics of Nikons as much, but with Canon DSLRs, a stop of under-exposure causes more noise than a stop higher ISO. It really isn't the ISO setting, per se, that is the root of noise, but the amount of light hitting the sensor, as is determined in each shot by the lighting, and the f-stop and shutter speed. There is at least a couple stops of exposure lattitude in each shot, where the image looks like it is in the ballpark for proper exposure. Those two stops vary the noise by 4x, whereas two stops of ISO difference might vary the noise by only 2x, or less. It is therefore essential that you learn to expose as high as possible without clipping desired highlights, to minimize noise.
Two people could go out and shoot all day at ISO 400 with your camera, I think, and one could have clean pictures, and another noisy. The one who leans toward under-exposure (or even standard exposure) will always get more noise.