Sodium in PDB 6yu6: Crystal Structure of Mhst in Complex with L-Leucine
Protein crystallography data
The structure of Crystal Structure of Mhst in Complex with L-Leucine, PDB code: 6yu6
was solved by
D.Focht,
C.Neumann,
J.Lyons,
A.Eguskiza Bilbao,
R.Blunck,
L.Malinauskaite,
I.O.Schwarz,
J.A.Javitch,
M.Quick,
P.Nissen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.48 /
2.35
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.230,
215.560,
50.170,
90.00,
90.05,
90.00
|
R / Rfree (%)
|
18.5 /
22.2
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Mhst in Complex with L-Leucine
(pdb code 6yu6). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of Mhst in Complex with L-Leucine, PDB code: 6yu6:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6yu6
Go back to
Sodium Binding Sites List in 6yu6
Sodium binding site 1 out
of 4 in the Crystal Structure of Mhst in Complex with L-Leucine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Mhst in Complex with L-Leucine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:32.6
occ:1.00
|
O
|
A:ALA320
|
2.0
|
30.6
|
1.0
|
O
|
A:VAL27
|
2.1
|
30.8
|
1.0
|
O
|
A:GLY24
|
2.3
|
41.2
|
1.0
|
OG
|
A:SER324
|
2.4
|
28.2
|
1.0
|
OG
|
A:SER323
|
2.4
|
35.4
|
1.0
|
C
|
A:ALA320
|
3.0
|
31.9
|
1.0
|
N
|
A:SER324
|
3.1
|
35.8
|
1.0
|
C
|
A:VAL27
|
3.1
|
29.7
|
1.0
|
C
|
A:GLY24
|
3.4
|
32.0
|
1.0
|
CB
|
A:SER324
|
3.4
|
28.2
|
1.0
|
CA
|
A:ALA320
|
3.5
|
33.3
|
1.0
|
CB
|
A:SER323
|
3.6
|
29.0
|
1.0
|
CA
|
A:SER324
|
3.7
|
32.0
|
1.0
|
C
|
A:SER323
|
3.7
|
31.4
|
1.0
|
CA
|
A:GLY28
|
3.8
|
36.6
|
1.0
|
N
|
A:GLY28
|
3.9
|
30.6
|
1.0
|
CB
|
A:ALA320
|
3.9
|
34.4
|
1.0
|
CA
|
A:SER323
|
4.1
|
28.2
|
1.0
|
CA
|
A:GLY24
|
4.1
|
35.0
|
1.0
|
N
|
A:ALA321
|
4.2
|
31.5
|
1.0
|
CA
|
A:VAL27
|
4.2
|
28.2
|
1.0
|
N
|
A:VAL27
|
4.2
|
30.4
|
1.0
|
N
|
A:SER323
|
4.2
|
31.6
|
1.0
|
O
|
A:SER25
|
4.4
|
37.7
|
1.0
|
N
|
A:SER25
|
4.4
|
28.9
|
1.0
|
C
|
A:SER25
|
4.4
|
34.6
|
1.0
|
O
|
A:SER323
|
4.6
|
29.5
|
1.0
|
CA
|
A:SER25
|
4.6
|
28.8
|
1.0
|
CA
|
A:ALA321
|
4.6
|
31.6
|
1.0
|
CB
|
A:VAL27
|
4.7
|
32.3
|
1.0
|
O
|
A:MET23
|
4.8
|
32.0
|
1.0
|
O
|
A:ALA319
|
4.8
|
33.2
|
1.0
|
C
|
A:ALA321
|
4.9
|
31.7
|
1.0
|
N
|
A:ALA320
|
4.9
|
34.4
|
1.0
|
C
|
A:ALA26
|
4.9
|
29.4
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6yu6
Go back to
Sodium Binding Sites List in 6yu6
Sodium binding site 2 out
of 4 in the Crystal Structure of Mhst in Complex with L-Leucine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Mhst in Complex with L-Leucine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:38.0
occ:1.00
|
O
|
A:ALA26
|
2.2
|
41.0
|
1.0
|
OXT
|
A:LEU503
|
2.4
|
33.9
|
1.0
|
OG1
|
A:THR231
|
2.4
|
38.9
|
1.0
|
OD1
|
A:ASP263
|
2.4
|
37.7
|
1.0
|
O
|
A:THR231
|
2.4
|
39.9
|
1.0
|
OD1
|
A:ASN31
|
2.4
|
36.3
|
1.0
|
ND2
|
A:ASN31
|
2.9
|
30.2
|
1.0
|
CG
|
A:ASN31
|
3.0
|
30.6
|
1.0
|
C
|
A:THR231
|
3.2
|
40.9
|
1.0
|
CA
|
A:THR231
|
3.3
|
41.8
|
1.0
|
CG
|
A:ASP263
|
3.3
|
38.3
|
1.0
|
C
|
A:ALA26
|
3.3
|
29.4
|
1.0
|
CB
|
A:THR231
|
3.4
|
36.6
|
1.0
|
C
|
A:LEU503
|
3.5
|
34.5
|
1.0
|
OD2
|
A:ASP263
|
3.5
|
43.8
|
1.0
|
N
|
A:LEU503
|
3.9
|
37.3
|
1.0
|
N
|
A:VAL27
|
4.1
|
30.4
|
1.0
|
CA
|
A:VAL27
|
4.2
|
28.2
|
1.0
|
CA
|
A:ALA26
|
4.2
|
28.2
|
1.0
|
O
|
A:LEU503
|
4.3
|
36.3
|
1.0
|
N
|
A:GLY28
|
4.3
|
30.6
|
1.0
|
CA
|
A:LEU503
|
4.3
|
39.9
|
1.0
|
CB
|
A:ASN31
|
4.3
|
30.2
|
1.0
|
N
|
A:ASN31
|
4.4
|
36.2
|
1.0
|
CG2
|
A:THR231
|
4.4
|
35.2
|
1.0
|
N
|
A:LEU232
|
4.5
|
37.4
|
1.0
|
CB
|
A:ALA26
|
4.6
|
28.2
|
1.0
|
CB
|
A:ASP263
|
4.6
|
38.2
|
1.0
|
N
|
A:THR231
|
4.7
|
36.7
|
1.0
|
CA
|
A:ASN31
|
4.7
|
34.5
|
1.0
|
C
|
A:GLY30
|
4.7
|
31.4
|
1.0
|
C
|
A:VAL27
|
4.8
|
29.7
|
1.0
|
O
|
A:PHE230
|
5.0
|
39.7
|
1.0
|
CA
|
A:GLY30
|
5.0
|
31.9
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6yu6
Go back to
Sodium Binding Sites List in 6yu6
Sodium binding site 3 out
of 4 in the Crystal Structure of Mhst in Complex with L-Leucine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Mhst in Complex with L-Leucine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:32.8
occ:1.00
|
O
|
B:ALA26
|
2.2
|
36.5
|
1.0
|
OG1
|
B:THR231
|
2.3
|
38.2
|
1.0
|
OD1
|
B:ASP263
|
2.4
|
40.0
|
1.0
|
OXT
|
B:LEU503
|
2.4
|
34.0
|
1.0
|
O
|
B:THR231
|
2.4
|
43.0
|
1.0
|
OD1
|
B:ASN31
|
2.4
|
38.2
|
1.0
|
CG
|
B:ASN31
|
3.0
|
35.4
|
1.0
|
C
|
B:ALA26
|
3.2
|
31.3
|
1.0
|
C
|
B:THR231
|
3.2
|
36.1
|
1.0
|
ND2
|
B:ASN31
|
3.2
|
43.1
|
1.0
|
CA
|
B:THR231
|
3.2
|
34.6
|
1.0
|
CG
|
B:ASP263
|
3.3
|
41.0
|
1.0
|
CB
|
B:THR231
|
3.3
|
37.2
|
1.0
|
OD2
|
B:ASP263
|
3.4
|
45.4
|
1.0
|
C
|
B:LEU503
|
3.5
|
33.9
|
1.0
|
N
|
B:LEU503
|
3.9
|
35.2
|
1.0
|
N
|
B:VAL27
|
4.0
|
35.2
|
1.0
|
CA
|
B:VAL27
|
4.1
|
28.6
|
1.0
|
CA
|
B:ALA26
|
4.1
|
30.4
|
1.0
|
N
|
B:ASN31
|
4.2
|
37.2
|
1.0
|
CB
|
B:ASN31
|
4.3
|
31.9
|
1.0
|
O
|
B:LEU503
|
4.3
|
32.3
|
1.0
|
N
|
B:GLY28
|
4.3
|
29.5
|
1.0
|
CA
|
B:LEU503
|
4.3
|
32.4
|
1.0
|
CG2
|
B:THR231
|
4.4
|
35.0
|
1.0
|
CB
|
B:ALA26
|
4.5
|
29.4
|
1.0
|
N
|
B:LEU232
|
4.5
|
36.5
|
1.0
|
C
|
B:VAL27
|
4.6
|
28.2
|
1.0
|
CA
|
B:ASN31
|
4.6
|
36.9
|
1.0
|
N
|
B:THR231
|
4.7
|
35.5
|
1.0
|
CB
|
B:ASP263
|
4.7
|
35.8
|
1.0
|
C
|
B:GLY30
|
4.7
|
36.3
|
1.0
|
CA
|
B:GLY30
|
4.9
|
28.2
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6yu6
Go back to
Sodium Binding Sites List in 6yu6
Sodium binding site 4 out
of 4 in the Crystal Structure of Mhst in Complex with L-Leucine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Mhst in Complex with L-Leucine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na502
b:29.6
occ:1.00
|
O
|
B:ALA320
|
2.1
|
30.3
|
1.0
|
O
|
B:VAL27
|
2.1
|
30.0
|
1.0
|
O
|
B:GLY24
|
2.2
|
36.4
|
1.0
|
OG
|
B:SER323
|
2.4
|
38.3
|
1.0
|
OG
|
B:SER324
|
2.4
|
33.8
|
1.0
|
C
|
B:ALA320
|
3.0
|
34.3
|
1.0
|
N
|
B:SER324
|
3.2
|
35.9
|
1.0
|
C
|
B:VAL27
|
3.3
|
28.2
|
1.0
|
C
|
B:GLY24
|
3.3
|
33.2
|
1.0
|
CA
|
B:ALA320
|
3.4
|
32.0
|
1.0
|
CB
|
B:SER324
|
3.5
|
30.1
|
1.0
|
CB
|
B:SER323
|
3.6
|
32.5
|
1.0
|
CA
|
B:SER324
|
3.8
|
32.2
|
1.0
|
CB
|
B:ALA320
|
3.8
|
35.4
|
1.0
|
C
|
B:SER323
|
3.8
|
30.4
|
1.0
|
CA
|
B:GLY24
|
4.0
|
36.6
|
1.0
|
CA
|
B:GLY28
|
4.1
|
28.9
|
1.0
|
CA
|
B:SER323
|
4.1
|
29.2
|
1.0
|
N
|
B:GLY28
|
4.2
|
29.5
|
1.0
|
N
|
B:ALA321
|
4.2
|
33.5
|
1.0
|
N
|
B:SER323
|
4.4
|
34.8
|
1.0
|
CA
|
B:VAL27
|
4.4
|
28.6
|
1.0
|
N
|
B:SER25
|
4.4
|
32.7
|
1.0
|
N
|
B:VAL27
|
4.5
|
35.2
|
1.0
|
O
|
B:SER25
|
4.6
|
34.0
|
1.0
|
O
|
B:SER323
|
4.6
|
30.5
|
1.0
|
C
|
B:SER25
|
4.7
|
29.8
|
1.0
|
CA
|
B:SER25
|
4.7
|
28.2
|
1.0
|
CB
|
B:VAL27
|
4.7
|
32.0
|
1.0
|
O
|
B:ALA319
|
4.7
|
42.4
|
1.0
|
CA
|
B:ALA321
|
4.7
|
28.2
|
1.0
|
N
|
B:ALA320
|
4.8
|
31.6
|
1.0
|
O
|
B:MET23
|
5.0
|
40.9
|
1.0
|
C
|
B:ALA321
|
5.0
|
31.7
|
1.0
|
|
Reference:
D.Focht,
C.Neumann,
J.Lyons,
A.Eguskiza Bilbao,
R.Blunck,
L.Malinauskaite,
I.O.Schwarz,
J.A.Javitch,
M.Quick,
P.Nissen.
Role of A Non-Helical Region of Transmembrane Helix 6 in the Substrate Recognition Mechanism of the Hydrophobic Amino Acid Transporter Mhst. To Be Published.
Page generated: Tue Oct 8 15:14:40 2024
|