Table 1.

Summary of the simulated systems and main results.

System	Distance (Å)		State	Na+	Supporting Information
	F76--S422	F76--S429
Free state
hDAT(59–604)	10.7±0.5	16.1±0.5	IF	None	Fig. S5
hDAT(25–604) (Model1)	8.4±0.5	12.3±0.9	IF	None	Fig. S5
hDAT(25–604) (Model2)	9.8±0.5	14.7±0.6	IF	None	Fig. S5
hDAT(1–604) (Model1)	9.5±0.6	14.0±0.5	IF	None	Fig. 3; Fig. S6
hDAT(1–604) (Model2)	4.3±0.3	11.4±0.3	OF	Na2	Fig.3
p-hDAT((1–604)) (Model1)	9.0±0.7	13.9±0.6	IF	Na1	Figs. S7-S9
p-hDAT((1–604)) (Model2)	8.9±0.4	14.2±0.5	IF	Na2	Figs. S7-S9
In complex with AMPH
hDAT(59–604)	4.4±0.2	11.7±0.3	OF	Na1; Na2	Fig. S10; Fig. S11
hDAT(25–604) (Model1)	4.7±0.3	12.3±0.4	OF	Na1; Na2	Fig. S10
hDAT(25–604) (Model2)	8.4±0.5	13.4±0.6	IF	Na2	Fig. S10
hDAT(1–604) (Model1)	8.6±0.4	14.0±0.7	IF	Na2	Fig. S12; Fig. S14
hDAT(1–604) (Model2)	7.7±0.4	12.8±0.6	IF	Na2	Fig. S12; Fig. S14
p-hDAT(1–604) (Model1)	4.4±0.3	11.0±0.5	OF	Na2	Fig. S13; Fig. S14
p-hDAT(1–604) (Model2)	8.4±0.4	13.9±0.5	IF	Na1; Na2	Fig. S13; Fig. S14
With C-terminal/Full-length
hDAT(59–620) (free state)	4.2±0.3	11.4±0.4	OF	None	Fig. S15
hDAT(1–620) (Model2, free state)	10.1±0.4	15.2±0.5	IF	Na1; Na2	Fig. S15
p-hDAT(1–620) + AMPH (Model1)	4.4±0.3	11.0±0.6	OF	Na2	Fig. S15
hDAT(1–620) (designed)	4.7±0.4	111.3±0.6	OF	Na2	Fig. S16

Notes:

⁽¹⁾The distances of F76--S422 and F76--S429 are averaged over the last 500-ns trajectory of each simulation

⁽²⁾Model1 and Mode2 correspond to the initial conformation of hDAT(1–604) shown in Fig. 1.

⁽³⁾Na⁺ denotes the sodium ions remained in the initial binding sites. The coordination environments of Na1 and Na2 are shown in Fig. S28 and Fig. S2. None indicates the release of both Na1 and Na2.

⁽⁴⁾IF and OF refer to the inward-facing open (or inward-open for simplicity) and outward-facing open (or outward-open for simplicity) conformation (or state), respectively.

⁽⁵⁾For the artificially designed full-length hDAT, the C-terminal tail was initially placed inside the membrane.