Sodium in PDB 6rf0: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form
Protein crystallography data
The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form, PDB code: 6rf0
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)
|
47.32 /
3.00
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.184,
239.719,
131.909,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.7 /
25.2
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form
(pdb code 6rf0). 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 "Dry" Form, PDB code: 6rf0:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 6rf0
Go back to
Sodium Binding Sites List in 6rf0
Sodium binding site 1 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form
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 "Dry" Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na301
b:41.0
occ:1.00
|
O
|
A:PHE86
|
2.3
|
34.9
|
1.0
|
OD1
|
B:ASP102
|
2.5
|
70.2
|
1.0
|
O
|
A:THR83
|
2.5
|
33.9
|
1.0
|
OH
|
A:TYR25
|
2.7
|
38.7
|
1.0
|
OD2
|
B:ASP102
|
2.9
|
56.1
|
1.0
|
CG
|
B:ASP102
|
3.1
|
62.6
|
1.0
|
C
|
A:PHE86
|
3.4
|
34.0
|
1.0
|
CZ
|
A:TYR25
|
3.6
|
35.4
|
1.0
|
C
|
A:THR83
|
3.7
|
32.8
|
1.0
|
CE1
|
A:TYR25
|
4.0
|
34.0
|
1.0
|
CA
|
A:THR87
|
4.1
|
40.0
|
1.0
|
N
|
A:THR87
|
4.2
|
33.5
|
1.0
|
CA
|
A:THR83
|
4.3
|
32.2
|
1.0
|
N
|
A:PHE86
|
4.5
|
35.0
|
1.0
|
CE2
|
A:TYR25
|
4.5
|
37.8
|
1.0
|
CA
|
A:PHE86
|
4.5
|
37.1
|
1.0
|
CB
|
B:ASP102
|
4.6
|
51.9
|
1.0
|
OG1
|
A:THR87
|
4.7
|
52.0
|
1.0
|
O
|
B:SER100
|
4.7
|
92.6
|
1.0
|
N
|
A:SER84
|
4.8
|
33.2
|
1.0
|
CB
|
A:THR83
|
4.8
|
33.6
|
1.0
|
CD2
|
A:TYR95
|
4.8
|
38.4
|
1.0
|
CB
|
A:THR87
|
4.9
|
39.6
|
1.0
|
CE2
|
A:TYR95
|
4.9
|
38.7
|
1.0
|
C
|
A:SER84
|
5.0
|
41.2
|
1.0
|
|
Sodium binding site 2 out
of 5 in 6rf0
Go back to
Sodium Binding Sites List in 6rf0
Sodium binding site 2 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form
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 "Dry" Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na304
b:35.6
occ:1.00
|
O
|
E:THR83
|
2.4
|
21.6
|
1.0
|
O
|
E:PHE86
|
2.5
|
29.7
|
1.0
|
OD2
|
A:ASP102
|
2.7
|
60.7
|
1.0
|
OD1
|
A:ASP102
|
2.8
|
52.8
|
1.0
|
OH
|
E:TYR25
|
3.0
|
44.5
|
1.0
|
CG
|
A:ASP102
|
3.1
|
60.0
|
1.0
|
C
|
E:THR83
|
3.6
|
24.9
|
1.0
|
C
|
E:PHE86
|
3.6
|
28.7
|
1.0
|
CZ
|
E:TYR25
|
3.9
|
37.6
|
1.0
|
CA
|
E:THR87
|
4.2
|
35.0
|
1.0
|
CA
|
E:THR83
|
4.3
|
25.7
|
1.0
|
N
|
E:THR87
|
4.3
|
29.6
|
1.0
|
CE1
|
E:TYR25
|
4.4
|
37.4
|
1.0
|
OG1
|
E:THR87
|
4.5
|
44.1
|
1.0
|
N
|
E:SER84
|
4.6
|
30.6
|
1.0
|
CB
|
A:ASP102
|
4.6
|
47.4
|
1.0
|
N
|
E:PHE86
|
4.6
|
34.9
|
1.0
|
O
|
A:SER100
|
4.6
|
0.8
|
1.0
|
CA
|
E:PHE86
|
4.7
|
31.5
|
1.0
|
CA
|
E:SER84
|
4.7
|
36.7
|
1.0
|
CB
|
E:THR83
|
4.8
|
25.8
|
1.0
|
C
|
E:SER84
|
4.8
|
34.3
|
1.0
|
CE2
|
E:TYR25
|
4.9
|
38.1
|
1.0
|
CB
|
E:THR87
|
4.9
|
32.3
|
1.0
|
|
Sodium binding site 3 out
of 5 in 6rf0
Go back to
Sodium Binding Sites List in 6rf0
Sodium binding site 3 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form
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 "Dry" Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na301
b:25.2
occ:1.00
|
O
|
B:THR83
|
2.2
|
33.1
|
1.0
|
O
|
B:PHE86
|
2.3
|
42.1
|
1.0
|
OH
|
B:TYR25
|
2.5
|
46.4
|
1.0
|
OD2
|
C:ASP102
|
2.7
|
61.5
|
1.0
|
OD1
|
C:ASP102
|
2.9
|
61.2
|
1.0
|
CG
|
C:ASP102
|
3.1
|
59.4
|
1.0
|
C
|
B:THR83
|
3.3
|
29.3
|
1.0
|
CZ
|
B:TYR25
|
3.4
|
48.9
|
1.0
|
C
|
B:PHE86
|
3.5
|
39.2
|
1.0
|
CE1
|
B:TYR25
|
3.9
|
50.6
|
1.0
|
CA
|
B:THR83
|
3.9
|
29.0
|
1.0
|
CA
|
B:THR87
|
4.3
|
43.3
|
1.0
|
N
|
B:THR87
|
4.3
|
41.2
|
1.0
|
N
|
B:PHE86
|
4.4
|
39.2
|
1.0
|
CE2
|
B:TYR25
|
4.4
|
55.5
|
1.0
|
CB
|
B:THR83
|
4.5
|
29.2
|
1.0
|
N
|
B:SER84
|
4.5
|
31.2
|
1.0
|
CA
|
B:PHE86
|
4.5
|
41.0
|
1.0
|
CB
|
C:ASP102
|
4.6
|
44.9
|
1.0
|
C
|
B:SER84
|
4.8
|
37.6
|
1.0
|
CA
|
B:SER84
|
4.9
|
35.7
|
1.0
|
OG1
|
B:THR87
|
4.9
|
50.9
|
1.0
|
CD2
|
B:TYR95
|
5.0
|
34.0
|
1.0
|
|
Sodium binding site 4 out
of 5 in 6rf0
Go back to
Sodium Binding Sites List in 6rf0
Sodium binding site 4 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form
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 "Dry" Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na301
b:32.4
occ:1.00
|
O
|
C:THR83
|
2.2
|
37.9
|
1.0
|
O
|
C:PHE86
|
2.3
|
44.0
|
1.0
|
OH
|
C:TYR25
|
2.5
|
43.1
|
1.0
|
OD1
|
D:ASP102
|
3.0
|
57.5
|
1.0
|
OD2
|
D:ASP102
|
3.0
|
42.6
|
1.0
|
C
|
C:THR83
|
3.3
|
31.1
|
1.0
|
CG
|
D:ASP102
|
3.3
|
48.3
|
1.0
|
CZ
|
C:TYR25
|
3.4
|
47.1
|
1.0
|
C
|
C:PHE86
|
3.5
|
37.4
|
1.0
|
CE1
|
C:TYR25
|
3.9
|
45.6
|
1.0
|
CA
|
C:THR83
|
3.9
|
30.4
|
1.0
|
CA
|
C:THR87
|
4.4
|
40.6
|
1.0
|
N
|
C:THR87
|
4.4
|
34.2
|
1.0
|
N
|
C:SER84
|
4.4
|
35.1
|
1.0
|
N
|
C:PHE86
|
4.4
|
37.1
|
1.0
|
CB
|
C:THR83
|
4.4
|
28.8
|
1.0
|
CE2
|
C:TYR25
|
4.5
|
46.7
|
1.0
|
CA
|
C:PHE86
|
4.5
|
40.8
|
1.0
|
CA
|
C:SER84
|
4.7
|
37.9
|
1.0
|
C
|
C:SER84
|
4.8
|
40.0
|
1.0
|
CB
|
D:ASP102
|
4.8
|
41.6
|
1.0
|
OG1
|
C:THR87
|
4.9
|
49.9
|
1.0
|
CD2
|
C:TYR95
|
5.0
|
37.9
|
1.0
|
|
Sodium binding site 5 out
of 5 in 6rf0
Go back to
Sodium Binding Sites List in 6rf0
Sodium binding site 5 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form
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 "Dry" Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na301
b:40.2
occ:1.00
|
O
|
D:THR83
|
2.4
|
31.2
|
1.0
|
O
|
D:PHE86
|
2.5
|
61.5
|
1.0
|
OD2
|
E:ASP102
|
2.6
|
52.9
|
1.0
|
OD1
|
E:ASP102
|
2.8
|
48.7
|
1.0
|
OH
|
D:TYR25
|
3.0
|
42.3
|
1.0
|
CG
|
E:ASP102
|
3.0
|
55.4
|
1.0
|
C
|
D:PHE86
|
3.6
|
44.1
|
1.0
|
C
|
D:THR83
|
3.6
|
29.7
|
1.0
|
CZ
|
D:TYR25
|
4.0
|
42.0
|
1.0
|
CA
|
D:THR87
|
4.1
|
39.3
|
1.0
|
N
|
D:THR87
|
4.3
|
42.0
|
1.0
|
CA
|
D:THR83
|
4.4
|
31.5
|
1.0
|
OG1
|
D:THR87
|
4.4
|
44.8
|
1.0
|
O
|
E:SER100
|
4.5
|
95.0
|
1.0
|
CE2
|
D:TYR25
|
4.5
|
47.1
|
1.0
|
CB
|
E:ASP102
|
4.5
|
42.0
|
1.0
|
N
|
D:PHE86
|
4.6
|
38.0
|
1.0
|
N
|
D:SER84
|
4.6
|
30.2
|
1.0
|
CA
|
D:PHE86
|
4.7
|
37.0
|
1.0
|
CA
|
D:SER84
|
4.8
|
32.5
|
1.0
|
C
|
D:SER84
|
4.8
|
35.8
|
1.0
|
CB
|
D:THR87
|
4.8
|
36.4
|
1.0
|
CB
|
D:THR83
|
4.9
|
29.8
|
1.0
|
O
|
D:SER84
|
5.0
|
49.5
|
1.0
|
CE1
|
D:TYR25
|
5.0
|
35.6
|
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 Oct 8 13:07:41 2024
|