Table 2 Na+-binding site integrity in different states of BetP measured as the distance between coordinating groups in X-ray crystallographic structures and during molecular dynamics simulations thereof.

From: Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na+ coupling

State

System

d (Na1′)

Δ d (Na1′)

d(Na2)

Δd(Na2)

CcS

4AIN-B

4.7

NA

3.8

NA

 

MD*

4.7±0.3

0.0

3.5±0.2

−0.3

Cc

4AIN-A

4.8

0.1

5.0

1.2

CeS

4LLH-A

4.9

0.2

4.7

0.9

 

4LLH-B

4.7

0.0

3.7

−0.1

 

MD

5.8±0.5

1.1

4.0±0.5

0.2

Ce

4DOJ-B

6.7

2.0

5.9

2.1

 

MD

5.8±0.4

1.1

6.1±1.4

2.3

CiS

4DOJ-C

8.0

3.3

7.7

3.9

 

4LHH-C

8.0

3.3

7.5

3.7

 

3PO3-C

8.3

3.6

7.4

3.6

Ci

3PO3-A

8.9

3.6

6.9

3.1

 

3PO3-B

6.8

2.1

7.3

3.5

  1. NA, not applicable.
  2. Systems are either crystal structures, listed as PDB and chain identifier, or mean±s.d. computed over three 100-ns molecular dynamics simulations of those structures, where available.
  3. *Simulations of CcS state described previously10. Ion-binding sites are defined as follows: for Na1, the distance (in Å) between T250 side-chain oxygen (TMH3′) and the center of the F380 (TMH5′) phenyl ring; for Na2, the distance between the carbonyl oxygen atoms of M150 (TMH1′) and F464 (TMH8′). The difference in binding site distances (Δd) is calculated relative to the value for the CcS state in 4AIN-B.
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