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I am planning to buy an MSI Radeon RX 6500 XT MECH 2X 4G OC graphics card and an ASUS PRIME B660M-A WIFI D4 motherboard. On the motherboard specs, it said :

Intel® 12th Gen Processors
1 x PCIe 4.0/3.0 x16 slot
Intel® B660 Chipset *
1 x PCIe 3.0 x16 slot (supports x4 mode)
1 x PCIe 3.0 x16 slot (supports x1 mode)
*Supports Intel® Optane Memory H Series on PCH-attached PCIe slot

Can I plug the graphics card into the first one (1 x PCIe 4.0/3.0 x16 slot) ? The graphics card has a PCIe 4.0 x4 interface.

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Yes

1x in the front means "1 piece", ie. there's one such slot on the motherboard.

PCI-e is very scalable and compatible - almost anything will work in a slot as long as it physically fits into it. This motherboard has three x16 (ie. full-sized) slots that will fit any PCI-e card.

This graphics card will run at its full performance in the 1st slot which has PCI-e 4.0 support and 4 lanes (actually more than that).

In the 2nd slot I would expect performance lower by a couple % due to it being wired to the 4 PCI-e lanes, but at version 3.0. The graphics card will work in 3.0 slots, but each lane will be limited to half its throughput.

Finally in the 3rd slot the card should work, but you'll see very significant performance loss. It will be running at 3.0 speeds and with only 1 out of 4 lanes connected, reducing the bandwidth 8-fold. While this may not be a problem for some computational workloads, in demanding games I would expect at least 30% performance drop.

TL;DR: use the 1st slot.

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