Sodium in PDB 6rex: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0
Protein crystallography data
The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0, PDB code: 6rex
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)
|
48.26 /
2.70
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.432,
240.787,
135.737,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.3 /
25
|
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 6.0
(pdb code 6rex). 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 6.0, PDB code: 6rex:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 6rex
Go back to
Sodium Binding Sites List in 6rex
Sodium binding site 1 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0
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 6.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na309
b:36.8
occ:1.00
|
O
|
A:HOH452
|
2.2
|
23.1
|
1.0
|
O
|
A:THR83
|
2.3
|
26.0
|
1.0
|
O
|
A:PHE86
|
2.4
|
30.0
|
1.0
|
OH
|
A:TYR25
|
2.6
|
25.7
|
1.0
|
OD1
|
B:ASP102
|
2.6
|
39.3
|
1.0
|
O
|
B:HOH448
|
2.8
|
37.9
|
1.0
|
CG
|
B:ASP102
|
3.3
|
37.5
|
1.0
|
OD2
|
B:ASP102
|
3.4
|
35.6
|
1.0
|
C
|
A:THR83
|
3.4
|
25.8
|
1.0
|
O
|
A:HOH447
|
3.5
|
29.1
|
1.0
|
C
|
A:PHE86
|
3.5
|
27.3
|
1.0
|
CZ
|
A:TYR25
|
3.6
|
25.0
|
1.0
|
O
|
B:HOH432
|
3.6
|
20.4
|
1.0
|
CA
|
A:THR83
|
3.9
|
26.3
|
1.0
|
CA
|
A:THR87
|
4.1
|
28.6
|
1.0
|
O
|
B:HOH406
|
4.1
|
30.1
|
1.0
|
CE1
|
A:TYR25
|
4.1
|
23.3
|
1.0
|
N
|
A:THR87
|
4.2
|
27.4
|
1.0
|
OG1
|
A:THR87
|
4.3
|
32.8
|
1.0
|
CB
|
A:THR83
|
4.4
|
25.2
|
1.0
|
CE2
|
A:TYR25
|
4.5
|
24.9
|
1.0
|
N
|
A:SER84
|
4.5
|
25.8
|
0.5
|
N
|
A:SER84
|
4.5
|
25.6
|
0.5
|
CA
|
A:PHE86
|
4.7
|
26.2
|
1.0
|
N
|
A:PHE86
|
4.7
|
26.6
|
1.0
|
CB
|
A:THR87
|
4.8
|
28.5
|
1.0
|
CB
|
B:ASP102
|
4.8
|
37.4
|
1.0
|
CD2
|
A:TYR95
|
4.8
|
25.4
|
1.0
|
CA
|
A:SER84
|
4.9
|
26.8
|
0.5
|
CA
|
A:SER84
|
5.0
|
26.5
|
0.5
|
|
Sodium binding site 2 out
of 5 in 6rex
Go back to
Sodium Binding Sites List in 6rex
Sodium binding site 2 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0
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 6.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na311
b:33.8
occ:1.00
|
O
|
B:HOH440
|
2.2
|
26.0
|
1.0
|
OD1
|
C:ASP102
|
2.3
|
45.1
|
1.0
|
O
|
B:THR83
|
2.4
|
39.8
|
1.0
|
OH
|
B:TYR25
|
2.6
|
24.5
|
1.0
|
O
|
B:PHE86
|
2.7
|
28.4
|
1.0
|
CG
|
C:ASP102
|
3.1
|
40.0
|
1.0
|
OD2
|
C:ASP102
|
3.2
|
39.1
|
1.0
|
O
|
C:HOH443
|
3.4
|
14.8
|
1.0
|
C
|
B:THR83
|
3.5
|
29.1
|
1.0
|
CZ
|
B:TYR25
|
3.6
|
25.7
|
1.0
|
O
|
C:HOH412
|
3.6
|
36.2
|
1.0
|
C
|
B:PHE86
|
3.8
|
29.2
|
1.0
|
CA
|
B:THR83
|
4.0
|
27.2
|
1.0
|
CE1
|
B:TYR25
|
4.2
|
23.6
|
1.0
|
CA
|
B:THR87
|
4.3
|
31.9
|
1.0
|
CB
|
B:THR83
|
4.3
|
26.6
|
1.0
|
OG1
|
B:THR87
|
4.4
|
29.2
|
1.0
|
CE2
|
B:TYR25
|
4.5
|
25.0
|
1.0
|
N
|
B:THR87
|
4.5
|
29.7
|
1.0
|
CB
|
C:ASP102
|
4.5
|
35.2
|
1.0
|
O
|
B:HOH439
|
4.6
|
29.1
|
1.0
|
N
|
B:SER84
|
4.6
|
30.1
|
0.5
|
N
|
B:SER84
|
4.6
|
29.5
|
0.5
|
O
|
C:SER100
|
4.8
|
38.0
|
1.0
|
N
|
C:ASP102
|
4.9
|
32.3
|
1.0
|
CD2
|
B:TYR95
|
4.9
|
27.6
|
1.0
|
CB
|
B:THR87
|
5.0
|
30.6
|
1.0
|
N
|
B:PHE86
|
5.0
|
28.6
|
1.0
|
CA
|
B:PHE86
|
5.0
|
30.1
|
1.0
|
|
Sodium binding site 3 out
of 5 in 6rex
Go back to
Sodium Binding Sites List in 6rex
Sodium binding site 3 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0
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 6.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na316
b:25.5
occ:1.00
|
O
|
C:THR83
|
2.3
|
24.8
|
1.0
|
O
|
C:HOH414
|
2.3
|
16.8
|
1.0
|
OD1
|
D:ASP102
|
2.4
|
37.3
|
1.0
|
OH
|
C:TYR25
|
2.5
|
26.2
|
1.0
|
O
|
C:PHE86
|
2.6
|
25.2
|
1.0
|
O
|
C:HOH455
|
2.8
|
37.8
|
1.0
|
CG
|
D:ASP102
|
3.1
|
34.9
|
1.0
|
OD2
|
D:ASP102
|
3.2
|
37.7
|
1.0
|
C
|
C:THR83
|
3.4
|
27.6
|
1.0
|
O
|
D:HOH405
|
3.4
|
22.7
|
1.0
|
CZ
|
C:TYR25
|
3.6
|
24.8
|
1.0
|
O
|
D:HOH416
|
3.6
|
19.0
|
1.0
|
C
|
C:PHE86
|
3.8
|
28.0
|
1.0
|
O
|
C:HOH466
|
3.9
|
31.0
|
1.0
|
CA
|
C:THR83
|
3.9
|
27.5
|
1.0
|
CE1
|
C:TYR25
|
4.2
|
24.2
|
1.0
|
CA
|
C:THR87
|
4.2
|
29.4
|
1.0
|
CB
|
C:THR83
|
4.3
|
25.6
|
1.0
|
CE2
|
C:TYR25
|
4.4
|
25.1
|
1.0
|
OG1
|
C:THR87
|
4.4
|
36.8
|
1.0
|
N
|
C:THR87
|
4.5
|
29.3
|
1.0
|
N
|
C:SER84
|
4.6
|
27.8
|
0.5
|
N
|
C:SER84
|
4.6
|
27.6
|
0.5
|
CB
|
D:ASP102
|
4.6
|
31.2
|
1.0
|
CD2
|
C:TYR95
|
4.9
|
28.1
|
1.0
|
N
|
C:PHE86
|
4.9
|
25.7
|
1.0
|
O
|
D:SER100
|
4.9
|
34.5
|
1.0
|
CA
|
C:PHE86
|
4.9
|
25.7
|
1.0
|
CB
|
C:THR87
|
4.9
|
31.8
|
1.0
|
CE2
|
C:TYR95
|
5.0
|
28.9
|
1.0
|
CG2
|
C:THR83
|
5.0
|
25.5
|
1.0
|
|
Sodium binding site 4 out
of 5 in 6rex
Go back to
Sodium Binding Sites List in 6rex
Sodium binding site 4 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0
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 6.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na313
b:35.0
occ:1.00
|
O
|
D:HOH424
|
2.1
|
46.2
|
1.0
|
OD1
|
E:ASP102
|
2.3
|
31.7
|
1.0
|
O
|
D:THR83
|
2.4
|
27.6
|
1.0
|
OH
|
D:TYR25
|
2.5
|
26.3
|
1.0
|
O
|
D:PHE86
|
2.5
|
29.3
|
1.0
|
CG
|
E:ASP102
|
3.1
|
34.3
|
1.0
|
OD2
|
E:ASP102
|
3.2
|
34.9
|
1.0
|
O
|
E:HOH414
|
3.2
|
20.2
|
1.0
|
CZ
|
D:TYR25
|
3.5
|
25.7
|
1.0
|
C
|
D:THR83
|
3.5
|
27.8
|
1.0
|
C
|
D:PHE86
|
3.7
|
24.4
|
1.0
|
O
|
E:HOH407
|
3.9
|
31.1
|
1.0
|
CA
|
D:THR83
|
4.0
|
28.6
|
1.0
|
CE1
|
D:TYR25
|
4.1
|
24.1
|
1.0
|
CA
|
D:THR87
|
4.2
|
27.9
|
1.0
|
CE2
|
D:TYR25
|
4.3
|
28.0
|
1.0
|
CB
|
D:THR83
|
4.4
|
28.4
|
1.0
|
N
|
D:THR87
|
4.4
|
24.9
|
1.0
|
OG1
|
D:THR87
|
4.4
|
38.5
|
1.0
|
CB
|
E:ASP102
|
4.5
|
33.1
|
1.0
|
N
|
D:SER84
|
4.7
|
25.9
|
0.5
|
N
|
D:SER84
|
4.7
|
25.6
|
0.5
|
CD2
|
D:TYR95
|
4.7
|
26.8
|
1.0
|
CA
|
D:PHE86
|
4.8
|
22.4
|
1.0
|
CE2
|
D:TYR95
|
4.9
|
27.7
|
1.0
|
N
|
D:PHE86
|
4.9
|
21.6
|
1.0
|
CB
|
D:THR87
|
4.9
|
29.0
|
1.0
|
N
|
E:ASP102
|
4.9
|
31.1
|
1.0
|
O
|
E:SER100
|
5.0
|
37.7
|
1.0
|
|
Sodium binding site 5 out
of 5 in 6rex
Go back to
Sodium Binding Sites List in 6rex
Sodium binding site 5 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0
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 6.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na311
b:34.5
occ:1.00
|
O
|
E:THR83
|
2.4
|
31.2
|
1.0
|
OD1
|
A:ASP102
|
2.5
|
36.9
|
1.0
|
O
|
E:PHE86
|
2.5
|
22.8
|
1.0
|
OH
|
E:TYR25
|
2.7
|
27.5
|
1.0
|
CG
|
A:ASP102
|
3.2
|
35.5
|
1.0
|
OD2
|
A:ASP102
|
3.3
|
33.0
|
1.0
|
C
|
E:THR83
|
3.5
|
28.9
|
1.0
|
O
|
E:HOH427
|
3.6
|
23.4
|
1.0
|
CZ
|
E:TYR25
|
3.6
|
28.9
|
1.0
|
C
|
E:PHE86
|
3.7
|
24.0
|
1.0
|
CA
|
E:THR83
|
4.0
|
27.7
|
1.0
|
CA
|
E:THR87
|
4.1
|
24.1
|
1.0
|
CE1
|
E:TYR25
|
4.3
|
27.5
|
1.0
|
OG1
|
E:THR87
|
4.3
|
25.4
|
1.0
|
N
|
E:THR87
|
4.3
|
23.5
|
1.0
|
CB
|
E:THR83
|
4.4
|
25.1
|
1.0
|
O
|
E:HOH466
|
4.4
|
37.6
|
1.0
|
CE2
|
E:TYR25
|
4.5
|
28.8
|
1.0
|
N
|
E:SER84
|
4.6
|
28.1
|
0.5
|
N
|
E:SER84
|
4.6
|
27.4
|
0.5
|
CB
|
A:ASP102
|
4.7
|
32.2
|
1.0
|
N
|
E:PHE86
|
4.8
|
22.3
|
1.0
|
CA
|
E:PHE86
|
4.8
|
23.8
|
1.0
|
CB
|
E:THR87
|
4.8
|
22.6
|
1.0
|
O
|
A:SER100
|
4.8
|
45.1
|
1.0
|
CD2
|
E:TYR95
|
4.9
|
25.0
|
1.0
|
CA
|
E:SER84
|
5.0
|
28.3
|
0.5
|
|
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 Oct 8 13:07:29 2024
|