Sodium in PDB 6rew: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0
Protein crystallography data
The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6rew
was solved by
K.Kovalev,
V.Polovinkin,
I.Gushchin,
V.Borshchevskiy,
V.Gordeliy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.03 /
2.20
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.360,
239.590,
135.250,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.9 /
17.2
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0
(pdb code 6rew). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6rew:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 6rew
Go back to
Sodium Binding Sites List in 6rew
Sodium binding site 1 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0
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 the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na315
b:26.3
occ:1.00
|
O
|
A:HOH450
|
2.3
|
21.6
|
1.0
|
O
|
A:PHE86
|
2.3
|
26.2
|
1.0
|
O
|
A:THR83
|
2.3
|
27.4
|
1.0
|
OH
|
A:TYR25
|
2.5
|
24.4
|
1.0
|
OD1
|
B:ASP102
|
2.5
|
29.9
|
1.0
|
O
|
B:HOH451
|
2.9
|
43.3
|
1.0
|
CG
|
B:ASP102
|
3.3
|
32.9
|
1.0
|
OD2
|
B:ASP102
|
3.3
|
34.3
|
1.0
|
C
|
A:THR83
|
3.3
|
24.1
|
1.0
|
CZ
|
A:TYR25
|
3.4
|
24.5
|
1.0
|
C
|
A:PHE86
|
3.5
|
22.9
|
1.0
|
O
|
B:HOH425
|
3.7
|
22.1
|
1.0
|
CA
|
A:THR83
|
3.8
|
25.8
|
1.0
|
CE1
|
A:TYR25
|
3.9
|
24.5
|
1.0
|
CA
|
A:THR87
|
4.1
|
26.9
|
1.0
|
OG1
|
A:THR87
|
4.2
|
37.8
|
1.0
|
CB
|
A:THR83
|
4.2
|
28.2
|
1.0
|
N
|
A:THR87
|
4.2
|
25.2
|
1.0
|
CE2
|
A:TYR25
|
4.4
|
24.2
|
1.0
|
N
|
A:SER84
|
4.5
|
21.6
|
0.5
|
N
|
A:SER84
|
4.5
|
22.1
|
0.5
|
CA
|
A:PHE86
|
4.6
|
21.9
|
1.0
|
N
|
A:PHE86
|
4.6
|
23.5
|
1.0
|
CB
|
B:ASP102
|
4.7
|
32.9
|
1.0
|
CD2
|
A:TYR95
|
4.8
|
24.5
|
1.0
|
CB
|
A:THR87
|
4.8
|
28.7
|
1.0
|
CE2
|
A:TYR95
|
4.9
|
24.1
|
1.0
|
CA
|
A:SER84
|
4.9
|
23.4
|
0.5
|
CA
|
A:SER84
|
5.0
|
24.4
|
0.5
|
|
Sodium binding site 2 out
of 5 in 6rew
Go back to
Sodium Binding Sites List in 6rew
Sodium binding site 2 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0
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 the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na313
b:24.7
occ:1.00
|
O
|
B:PHE86
|
2.3
|
24.2
|
1.0
|
O
|
B:HOH472
|
2.3
|
27.7
|
1.0
|
O
|
B:THR83
|
2.3
|
25.6
|
1.0
|
OH
|
B:TYR25
|
2.4
|
24.2
|
1.0
|
OD1
|
C:ASP102
|
2.5
|
27.3
|
1.0
|
O
|
C:HOH478
|
2.9
|
45.0
|
1.0
|
CG
|
C:ASP102
|
3.3
|
29.5
|
1.0
|
CZ
|
B:TYR25
|
3.3
|
24.6
|
1.0
|
OD2
|
C:ASP102
|
3.3
|
31.0
|
1.0
|
C
|
B:THR83
|
3.4
|
23.7
|
1.0
|
C
|
B:PHE86
|
3.5
|
21.7
|
1.0
|
O
|
C:HOH441
|
3.7
|
21.6
|
1.0
|
CA
|
B:THR83
|
3.8
|
24.3
|
1.0
|
CE1
|
B:TYR25
|
3.8
|
25.2
|
1.0
|
O
|
C:HOH404
|
4.1
|
44.3
|
1.0
|
CA
|
B:THR87
|
4.1
|
25.9
|
1.0
|
OG1
|
B:THR87
|
4.2
|
32.2
|
1.0
|
CB
|
B:THR83
|
4.2
|
24.9
|
1.0
|
N
|
B:THR87
|
4.2
|
22.9
|
1.0
|
O
|
B:HOH499
|
4.2
|
46.8
|
1.0
|
CE2
|
B:TYR25
|
4.3
|
25.2
|
1.0
|
N
|
B:SER84
|
4.5
|
23.1
|
0.5
|
N
|
B:SER84
|
4.5
|
23.0
|
0.5
|
CA
|
B:PHE86
|
4.6
|
22.2
|
1.0
|
N
|
B:PHE86
|
4.6
|
22.5
|
1.0
|
CD2
|
B:TYR95
|
4.7
|
23.7
|
1.0
|
CB
|
C:ASP102
|
4.7
|
26.8
|
1.0
|
CB
|
B:THR87
|
4.8
|
27.7
|
1.0
|
CE2
|
B:TYR95
|
4.9
|
25.6
|
1.0
|
O
|
B:TRP82
|
4.9
|
22.1
|
1.0
|
CA
|
B:SER84
|
5.0
|
24.2
|
0.5
|
CA
|
B:SER84
|
5.0
|
24.0
|
0.5
|
|
Sodium binding site 3 out
of 5 in 6rew
Go back to
Sodium Binding Sites List in 6rew
Sodium binding site 3 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0
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 the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na316
b:26.1
occ:1.00
|
O
|
C:HOH451
|
2.3
|
24.1
|
1.0
|
O
|
C:PHE86
|
2.3
|
24.2
|
1.0
|
O
|
C:THR83
|
2.3
|
22.7
|
1.0
|
OH
|
C:TYR25
|
2.5
|
25.4
|
1.0
|
OD1
|
D:ASP102
|
2.5
|
26.0
|
1.0
|
O
|
D:HOH444
|
2.9
|
43.5
|
1.0
|
CG
|
D:ASP102
|
3.3
|
28.3
|
1.0
|
OD2
|
D:ASP102
|
3.3
|
33.6
|
1.0
|
C
|
C:THR83
|
3.4
|
22.7
|
1.0
|
CZ
|
C:TYR25
|
3.4
|
24.2
|
1.0
|
C
|
C:PHE86
|
3.5
|
23.9
|
1.0
|
O
|
D:HOH415
|
3.7
|
23.2
|
1.0
|
CA
|
C:THR83
|
3.8
|
25.8
|
1.0
|
CE1
|
C:TYR25
|
3.9
|
24.1
|
1.0
|
O
|
C:HOH497
|
4.1
|
51.0
|
1.0
|
CA
|
C:THR87
|
4.1
|
29.2
|
1.0
|
OG1
|
C:THR87
|
4.2
|
37.0
|
1.0
|
N
|
C:THR87
|
4.2
|
23.7
|
1.0
|
CB
|
C:THR83
|
4.2
|
24.4
|
1.0
|
CE2
|
C:TYR25
|
4.3
|
20.8
|
1.0
|
N
|
C:SER84
|
4.5
|
23.5
|
0.5
|
N
|
C:SER84
|
4.5
|
22.0
|
0.5
|
CA
|
C:PHE86
|
4.6
|
24.0
|
1.0
|
N
|
C:PHE86
|
4.6
|
22.6
|
1.0
|
CB
|
D:ASP102
|
4.7
|
26.3
|
1.0
|
CD2
|
C:TYR95
|
4.7
|
22.7
|
1.0
|
CB
|
C:THR87
|
4.8
|
31.8
|
1.0
|
CE2
|
C:TYR95
|
4.9
|
24.5
|
1.0
|
CA
|
C:SER84
|
5.0
|
26.5
|
0.5
|
CA
|
C:SER84
|
5.0
|
23.9
|
0.5
|
O
|
C:TRP82
|
5.0
|
24.5
|
1.0
|
|
Sodium binding site 4 out
of 5 in 6rew
Go back to
Sodium Binding Sites List in 6rew
Sodium binding site 4 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0
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 the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na316
b:25.5
occ:1.00
|
O
|
D:PHE86
|
2.3
|
25.6
|
1.0
|
O
|
D:THR83
|
2.3
|
25.6
|
1.0
|
O
|
D:HOH438
|
2.4
|
24.1
|
1.0
|
OH
|
D:TYR25
|
2.4
|
23.4
|
1.0
|
OD1
|
E:ASP102
|
2.5
|
25.4
|
1.0
|
CG
|
E:ASP102
|
3.2
|
27.6
|
1.0
|
OD2
|
E:ASP102
|
3.3
|
30.9
|
1.0
|
C
|
D:THR83
|
3.3
|
24.5
|
1.0
|
CZ
|
D:TYR25
|
3.4
|
26.0
|
1.0
|
C
|
D:PHE86
|
3.5
|
23.4
|
1.0
|
O
|
E:HOH409
|
3.7
|
22.2
|
1.0
|
CA
|
D:THR83
|
3.8
|
25.1
|
1.0
|
CE1
|
D:TYR25
|
3.9
|
26.9
|
1.0
|
CA
|
D:THR87
|
4.0
|
30.3
|
0.5
|
CA
|
D:THR87
|
4.1
|
23.3
|
0.5
|
O
|
D:HOH487
|
4.1
|
46.0
|
1.0
|
OG1
|
D:THR87
|
4.2
|
26.2
|
0.5
|
CB
|
D:THR83
|
4.2
|
26.3
|
1.0
|
N
|
D:THR87
|
4.2
|
24.2
|
0.5
|
O
|
E:HOH402
|
4.2
|
42.7
|
1.0
|
N
|
D:THR87
|
4.2
|
20.5
|
0.5
|
CG2
|
D:THR87
|
4.3
|
38.1
|
0.5
|
CE2
|
D:TYR25
|
4.3
|
25.7
|
1.0
|
N
|
D:SER84
|
4.5
|
22.0
|
0.5
|
N
|
D:SER84
|
4.5
|
21.5
|
0.5
|
CA
|
D:PHE86
|
4.6
|
23.7
|
1.0
|
N
|
D:PHE86
|
4.6
|
22.2
|
1.0
|
CB
|
D:THR87
|
4.6
|
32.1
|
0.5
|
CB
|
E:ASP102
|
4.7
|
24.4
|
1.0
|
CD2
|
D:TYR95
|
4.7
|
22.3
|
1.0
|
CB
|
D:THR87
|
4.8
|
20.6
|
0.5
|
CE2
|
D:TYR95
|
4.9
|
24.2
|
1.0
|
CA
|
D:SER84
|
5.0
|
25.3
|
0.5
|
O
|
D:TRP82
|
5.0
|
22.6
|
1.0
|
|
Sodium binding site 5 out
of 5 in 6rew
Go back to
Sodium Binding Sites List in 6rew
Sodium binding site 5 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na315
b:25.5
occ:1.00
|
O
|
E:HOH453
|
2.3
|
28.2
|
1.0
|
O
|
E:THR83
|
2.3
|
24.1
|
1.0
|
O
|
E:PHE86
|
2.3
|
24.8
|
1.0
|
OH
|
E:TYR25
|
2.4
|
24.4
|
1.0
|
OD1
|
A:ASP102
|
2.5
|
28.4
|
1.0
|
CG
|
A:ASP102
|
3.3
|
27.6
|
1.0
|
OD2
|
A:ASP102
|
3.3
|
30.1
|
1.0
|
C
|
E:THR83
|
3.3
|
22.6
|
1.0
|
CZ
|
E:TYR25
|
3.4
|
24.1
|
1.0
|
C
|
E:PHE86
|
3.5
|
23.5
|
1.0
|
O
|
A:HOH428
|
3.8
|
23.3
|
1.0
|
CA
|
E:THR83
|
3.8
|
22.4
|
1.0
|
CE1
|
E:TYR25
|
3.9
|
23.8
|
1.0
|
CA
|
E:THR87
|
4.1
|
26.6
|
0.5
|
O
|
E:HOH501
|
4.1
|
49.6
|
1.0
|
CA
|
E:THR87
|
4.2
|
22.4
|
0.5
|
CB
|
E:THR83
|
4.2
|
20.9
|
1.0
|
OG1
|
E:THR87
|
4.2
|
26.6
|
0.5
|
N
|
E:THR87
|
4.2
|
24.2
|
0.5
|
N
|
E:THR87
|
4.3
|
21.6
|
0.5
|
CG2
|
E:THR87
|
4.3
|
32.9
|
0.5
|
CE2
|
E:TYR25
|
4.3
|
25.2
|
1.0
|
N
|
E:SER84
|
4.5
|
22.2
|
0.5
|
N
|
E:SER84
|
4.5
|
21.5
|
0.5
|
N
|
E:PHE86
|
4.6
|
24.0
|
1.0
|
CA
|
E:PHE86
|
4.6
|
22.5
|
1.0
|
CB
|
E:THR87
|
4.7
|
28.2
|
0.5
|
CB
|
A:ASP102
|
4.7
|
26.4
|
1.0
|
CD2
|
E:TYR95
|
4.8
|
22.2
|
1.0
|
CB
|
E:THR87
|
4.8
|
21.3
|
0.5
|
CA
|
E:SER84
|
4.9
|
23.7
|
0.5
|
CA
|
E:SER84
|
5.0
|
22.6
|
0.5
|
CE2
|
E:TYR95
|
5.0
|
21.2
|
1.0
|
O
|
E:TRP82
|
5.0
|
22.0
|
1.0
|
|
Reference:
K.Kovalev,
V.Polovinkin,
I.Gushchin,
A.Alekseev,
V.Shevchenko,
V.Borshchevskiy,
R.Astashkin,
T.Balandin,
D.Bratanov,
S.Vaganova,
A.Popov,
V.Chupin,
G.Buldt,
E.Bamberg,
V.Gordeliy.
Structure and Mechanisms of Sodium-Pumping KR2 Rhodopsin. Sci Adv V. 5 V2671 2019.
ISSN: ESSN 2375-2548
PubMed: 30989112
DOI: 10.1126/SCIADV.AAV2671
Page generated: Tue Dec 15 12:52:24 2020
|