I'd make some adjustments:
You were paying extra for the motherboard only to get lower performance. Swapped it for cheaper option (still very good) and swapped the RAM to DDR4. There is really no reason to go with DDR3 with Skylake CPUs and the original issue you had was that Skylake's memory controller operates at 1.35V, while standard DDR3 RAM operates at 1.5V. You'd be running at risk of instability and CPU damage.
I also swapped the SSD for better model (and this, unlike V300 isn't known for bait and switch tactic).
And finally I'd go with the RX 460 to stay near the budget.
However I'd advise to look at used hardware market, you might be able to find something better for same price.
PCPartPicker part list / Price breakdown by merchant
| Type | Item | Price |
|---|---|---|
| CPU | Intel Core i3-6100 3.7GHz Dual-Core Processor | $110.99 @ SuperBiiz |
| Motherboard | Asus H110M-A Micro ATX LGA1151 Motherboard | $59.99 @ SuperBiiz |
| Memory | Kingston FURY 8GB (1 x 8GB) DDR4-2400 Memory | $35.44 @ Amazon |
| Storage | SK hynix SL308 120GB 2.5" Solid State Drive | $44.99 @ SuperBiiz |
| Storage | Western Digital Caviar Blue 1TB 3.5" 7200RPM Internal Hard Drive | $61.19 @ Amazon |
| Video Card | Gigabyte Radeon RX 460 4GB WINDFORCE OC Video Card | $127.99 @ SuperBiiz |
| Case | Deepcool TESSERACT SW ATX Mid Tower Case | $39.99 @ SuperBiiz |
| Power Supply | EVGA 450W 80+ Bronze Certified ATX Power Supply | $38.99 @ SuperBiiz |
| Prices include shipping, taxes, rebates, and discounts | ||
| Total | $519.57 | |
| Generated by PCPartPicker 2016-09-26 04:09 EDT-0400 |