Sodium in PDB 6yc3: 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: 6yc3
was solved by
K.Kovalev,
I.Gushchin,
V.Gordeliy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.00
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.866,
240.323,
135.513,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.8 /
19.5
|
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 6yc3). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 10 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: 6yc3:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 1 out
of 10 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:Na321
b:39.8
occ:1.00
|
O
|
A:PHE86
|
2.3
|
38.9
|
1.0
|
O
|
A:HOH473
|
2.3
|
39.8
|
1.0
|
O
|
A:THR83
|
2.3
|
40.1
|
1.0
|
OH
|
A:TYR25
|
2.4
|
38.5
|
1.0
|
OD1
|
B:ASP102
|
2.5
|
41.9
|
1.0
|
O
|
B:HOH473
|
2.8
|
61.6
|
1.0
|
CG
|
B:ASP102
|
3.2
|
45.9
|
1.0
|
OD2
|
B:ASP102
|
3.3
|
46.1
|
1.0
|
CZ
|
A:TYR25
|
3.3
|
38.6
|
1.0
|
C
|
A:THR83
|
3.3
|
38.5
|
1.0
|
C
|
A:PHE86
|
3.5
|
35.2
|
1.0
|
O
|
B:HOH435
|
3.7
|
37.4
|
1.0
|
NA
|
B:NA316
|
3.8
|
76.3
|
1.0
|
CA
|
A:THR83
|
3.8
|
38.4
|
1.0
|
CE1
|
A:TYR25
|
3.8
|
39.7
|
1.0
|
O
|
A:HOH489
|
4.0
|
58.6
|
1.0
|
CA
|
A:THR87
|
4.2
|
40.5
|
1.0
|
N
|
A:THR87
|
4.3
|
37.3
|
1.0
|
CB
|
A:THR83
|
4.3
|
40.4
|
1.0
|
CE2
|
A:TYR25
|
4.3
|
36.4
|
1.0
|
OG1
|
A:THR87
|
4.4
|
46.4
|
1.0
|
N
|
A:SER84
|
4.5
|
40.1
|
0.5
|
N
|
A:SER84
|
4.5
|
36.5
|
0.2
|
N
|
A:SER84
|
4.5
|
36.5
|
0.2
|
CA
|
A:PHE86
|
4.6
|
33.0
|
1.0
|
N
|
A:PHE86
|
4.7
|
36.0
|
1.0
|
CB
|
B:ASP102
|
4.7
|
41.9
|
1.0
|
CD2
|
A:TYR95
|
4.7
|
35.1
|
1.0
|
O
|
A:HOH492
|
4.8
|
71.9
|
1.0
|
CB
|
A:THR87
|
4.9
|
39.1
|
1.0
|
CE2
|
A:TYR95
|
4.9
|
35.9
|
1.0
|
|
Sodium binding site 2 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 2 out
of 10 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
|
A:Na322
b:78.6
occ:1.00
|
O
|
A:HOH515
|
2.3
|
71.2
|
1.0
|
O
|
E:HOH517
|
2.4
|
67.0
|
1.0
|
O
|
A:SER100
|
2.5
|
44.0
|
1.0
|
O
|
A:HOH451
|
2.5
|
59.3
|
1.0
|
O
|
E:HOH479
|
2.5
|
42.2
|
1.0
|
O
|
A:HOH497
|
2.7
|
53.6
|
1.0
|
C
|
A:SER100
|
3.7
|
46.3
|
1.0
|
NA
|
E:NA318
|
3.8
|
39.3
|
1.0
|
O
|
E:HOH518
|
3.8
|
68.0
|
1.0
|
O
|
A:HOH405
|
3.9
|
61.8
|
1.0
|
CA
|
A:GLY101
|
4.1
|
38.5
|
1.0
|
OD1
|
A:ASP102
|
4.1
|
43.1
|
1.0
|
O
|
E:HOH499
|
4.1
|
75.3
|
1.0
|
O
|
E:THR83
|
4.2
|
39.0
|
1.0
|
C
|
A:GLY101
|
4.3
|
37.7
|
1.0
|
N
|
A:GLY101
|
4.3
|
40.3
|
1.0
|
O
|
A:HOH514
|
4.3
|
69.5
|
1.0
|
O
|
A:HOH435
|
4.5
|
35.1
|
1.0
|
O
|
A:HOH521
|
4.5
|
87.2
|
1.0
|
O
|
A:GLY101
|
4.6
|
44.5
|
1.0
|
CG
|
A:ASP102
|
4.7
|
39.8
|
1.0
|
O
|
E:HOH429
|
4.7
|
58.7
|
1.0
|
N
|
A:ASP102
|
4.7
|
33.8
|
1.0
|
CA
|
A:SER100
|
4.9
|
41.7
|
1.0
|
CG2
|
E:THR87
|
5.0
|
49.0
|
0.5
|
OD2
|
A:ASP102
|
5.0
|
43.4
|
1.0
|
OG1
|
E:THR87
|
5.0
|
41.3
|
0.5
|
|
Sodium binding site 3 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 3 out
of 10 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
|
B:Na315
b:39.1
occ:1.00
|
O
|
B:THR83
|
2.3
|
43.5
|
1.0
|
O
|
B:PHE86
|
2.3
|
38.2
|
1.0
|
O
|
B:HOH490
|
2.4
|
40.9
|
1.0
|
OH
|
B:TYR25
|
2.4
|
36.8
|
1.0
|
OD1
|
C:ASP102
|
2.5
|
39.7
|
1.0
|
O
|
C:HOH456
|
2.7
|
61.9
|
1.0
|
CG
|
C:ASP102
|
3.2
|
43.3
|
1.0
|
OD2
|
C:ASP102
|
3.3
|
46.6
|
1.0
|
C
|
B:THR83
|
3.3
|
39.6
|
1.0
|
CZ
|
B:TYR25
|
3.3
|
38.8
|
1.0
|
C
|
B:PHE86
|
3.5
|
36.3
|
1.0
|
O
|
C:HOH441
|
3.7
|
35.1
|
1.0
|
CA
|
B:THR83
|
3.8
|
41.4
|
1.0
|
CE1
|
B:TYR25
|
3.9
|
36.3
|
1.0
|
NA
|
C:NA320
|
3.9
|
70.9
|
1.0
|
O
|
B:HOH506
|
4.0
|
57.0
|
1.0
|
CA
|
B:THR87
|
4.2
|
37.4
|
1.0
|
N
|
B:THR87
|
4.2
|
36.2
|
1.0
|
CB
|
B:THR83
|
4.3
|
38.9
|
1.0
|
OG1
|
B:THR87
|
4.3
|
42.9
|
1.0
|
CE2
|
B:TYR25
|
4.3
|
36.1
|
1.0
|
N
|
B:SER84
|
4.5
|
36.9
|
0.2
|
N
|
B:SER84
|
4.5
|
40.3
|
0.5
|
N
|
B:SER84
|
4.5
|
38.2
|
0.2
|
CA
|
B:PHE86
|
4.6
|
37.6
|
1.0
|
N
|
B:PHE86
|
4.7
|
37.5
|
1.0
|
CB
|
C:ASP102
|
4.7
|
41.4
|
1.0
|
CD2
|
B:TYR95
|
4.8
|
37.6
|
1.0
|
CB
|
B:THR87
|
4.9
|
38.5
|
1.0
|
CE2
|
B:TYR95
|
5.0
|
39.4
|
1.0
|
|
Sodium binding site 4 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 4 out
of 10 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
|
B:Na316
b:76.3
occ:1.00
|
O
|
B:HOH502
|
2.1
|
69.5
|
1.0
|
O
|
A:HOH473
|
2.4
|
39.8
|
1.0
|
O
|
A:HOH489
|
2.4
|
58.6
|
1.0
|
O
|
B:SER100
|
2.4
|
44.1
|
1.0
|
O
|
B:HOH473
|
2.5
|
61.6
|
1.0
|
O
|
B:HOH485
|
2.9
|
60.4
|
1.0
|
C
|
B:SER100
|
3.6
|
43.0
|
1.0
|
NA
|
A:NA321
|
3.8
|
39.8
|
1.0
|
OD1
|
B:ASP102
|
4.0
|
41.9
|
1.0
|
O
|
B:HOH411
|
4.1
|
62.1
|
1.0
|
O
|
A:HOH492
|
4.1
|
71.9
|
1.0
|
CA
|
B:GLY101
|
4.1
|
37.5
|
1.0
|
O
|
B:HOH435
|
4.2
|
37.4
|
1.0
|
O
|
A:THR83
|
4.2
|
40.1
|
1.0
|
C
|
B:GLY101
|
4.3
|
36.4
|
1.0
|
N
|
B:GLY101
|
4.3
|
38.2
|
1.0
|
O
|
B:HOH503
|
4.5
|
88.9
|
1.0
|
O
|
B:GLY101
|
4.6
|
40.5
|
1.0
|
CG
|
B:ASP102
|
4.6
|
45.9
|
1.0
|
N
|
B:ASP102
|
4.6
|
35.3
|
1.0
|
CA
|
B:SER100
|
4.7
|
44.2
|
1.0
|
OG1
|
A:THR87
|
4.8
|
46.4
|
1.0
|
OD2
|
B:ASP102
|
4.9
|
46.1
|
1.0
|
O
|
A:HOH404
|
5.0
|
61.0
|
1.0
|
|
Sodium binding site 5 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 5 out
of 10 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
|
C:Na319
b:39.1
occ:1.00
|
O
|
C:THR83
|
2.3
|
38.1
|
1.0
|
O
|
C:PHE86
|
2.3
|
37.4
|
1.0
|
O
|
C:HOH466
|
2.4
|
40.7
|
1.0
|
OH
|
C:TYR25
|
2.4
|
39.6
|
1.0
|
OD1
|
D:ASP102
|
2.5
|
38.2
|
1.0
|
O
|
D:HOH435
|
2.8
|
55.1
|
1.0
|
CG
|
D:ASP102
|
3.2
|
40.7
|
1.0
|
OD2
|
D:ASP102
|
3.3
|
48.3
|
1.0
|
C
|
C:THR83
|
3.3
|
39.7
|
1.0
|
CZ
|
C:TYR25
|
3.4
|
35.0
|
1.0
|
C
|
C:PHE86
|
3.5
|
38.7
|
1.0
|
O
|
D:HOH425
|
3.7
|
35.9
|
1.0
|
CA
|
C:THR83
|
3.8
|
39.9
|
1.0
|
CE1
|
C:TYR25
|
3.9
|
35.9
|
1.0
|
O
|
C:HOH499
|
4.0
|
61.6
|
1.0
|
NA
|
D:NA319
|
4.1
|
71.5
|
1.0
|
CA
|
C:THR87
|
4.2
|
41.7
|
1.0
|
N
|
C:THR87
|
4.2
|
38.7
|
1.0
|
CB
|
C:THR83
|
4.2
|
36.3
|
1.0
|
OG1
|
C:THR87
|
4.3
|
48.4
|
1.0
|
CE2
|
C:TYR25
|
4.3
|
34.8
|
1.0
|
N
|
C:SER84
|
4.5
|
36.2
|
0.5
|
N
|
C:SER84
|
4.5
|
37.3
|
0.5
|
CA
|
C:PHE86
|
4.6
|
36.6
|
1.0
|
N
|
C:PHE86
|
4.7
|
34.5
|
1.0
|
CB
|
D:ASP102
|
4.7
|
39.3
|
1.0
|
CD2
|
C:TYR95
|
4.8
|
34.8
|
1.0
|
CB
|
C:THR87
|
4.9
|
44.6
|
1.0
|
CE2
|
C:TYR95
|
5.0
|
36.4
|
1.0
|
|
Sodium binding site 6 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 6 out
of 10 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 6 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:Na320
b:70.9
occ:1.00
|
O
|
C:HOH456
|
2.4
|
61.9
|
1.0
|
O
|
C:HOH512
|
2.5
|
67.2
|
1.0
|
O
|
C:SER100
|
2.5
|
38.9
|
1.0
|
O
|
B:HOH490
|
2.5
|
40.9
|
1.0
|
O
|
B:HOH506
|
2.6
|
57.0
|
1.0
|
O
|
C:HOH484
|
2.8
|
63.3
|
1.0
|
C
|
C:SER100
|
3.7
|
42.3
|
1.0
|
O
|
C:HOH503
|
3.7
|
66.8
|
1.0
|
NA
|
B:NA315
|
3.9
|
39.1
|
1.0
|
CA
|
C:GLY101
|
4.0
|
37.8
|
1.0
|
OD1
|
C:ASP102
|
4.1
|
39.7
|
1.0
|
C
|
C:GLY101
|
4.2
|
37.7
|
1.0
|
N
|
C:GLY101
|
4.3
|
38.6
|
1.0
|
O
|
C:HOH465
|
4.3
|
77.9
|
1.0
|
O
|
B:THR83
|
4.3
|
43.5
|
1.0
|
O
|
C:GLY101
|
4.5
|
45.7
|
1.0
|
O
|
C:HOH441
|
4.5
|
35.1
|
1.0
|
N
|
C:ASP102
|
4.7
|
36.3
|
1.0
|
CG
|
C:ASP102
|
4.7
|
43.3
|
1.0
|
CA
|
C:SER100
|
4.9
|
43.0
|
1.0
|
OD2
|
C:ASP102
|
4.9
|
46.6
|
1.0
|
|
Sodium binding site 7 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 7 out
of 10 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 7 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:Na318
b:38.8
occ:1.00
|
O
|
D:THR83
|
2.2
|
39.3
|
1.0
|
O
|
D:PHE86
|
2.3
|
37.7
|
1.0
|
O
|
D:HOH469
|
2.3
|
39.4
|
1.0
|
OH
|
D:TYR25
|
2.5
|
37.4
|
1.0
|
OD1
|
E:ASP102
|
2.5
|
40.5
|
1.0
|
O
|
E:HOH465
|
2.9
|
60.1
|
1.0
|
CG
|
E:ASP102
|
3.3
|
41.0
|
1.0
|
C
|
D:THR83
|
3.3
|
37.8
|
1.0
|
OD2
|
E:ASP102
|
3.3
|
47.5
|
1.0
|
CZ
|
D:TYR25
|
3.4
|
36.0
|
1.0
|
C
|
D:PHE86
|
3.5
|
36.5
|
1.0
|
O
|
E:HOH426
|
3.7
|
39.4
|
1.0
|
O
|
D:HOH474
|
3.7
|
62.0
|
1.0
|
CA
|
D:THR83
|
3.8
|
37.9
|
1.0
|
CE1
|
D:TYR25
|
3.9
|
38.8
|
1.0
|
CA
|
D:THR87
|
4.0
|
43.3
|
0.5
|
NA
|
E:NA319
|
4.1
|
66.1
|
1.0
|
CA
|
D:THR87
|
4.1
|
35.8
|
0.5
|
N
|
D:THR87
|
4.2
|
38.4
|
0.5
|
N
|
D:THR87
|
4.2
|
34.0
|
0.5
|
OG1
|
D:THR87
|
4.2
|
36.5
|
0.5
|
CB
|
D:THR83
|
4.2
|
37.7
|
1.0
|
CG2
|
D:THR87
|
4.3
|
50.0
|
0.5
|
CE2
|
D:TYR25
|
4.4
|
36.9
|
1.0
|
N
|
D:SER84
|
4.5
|
36.8
|
0.5
|
N
|
D:SER84
|
4.5
|
35.0
|
0.2
|
N
|
D:SER84
|
4.5
|
34.0
|
0.2
|
CA
|
D:PHE86
|
4.6
|
37.8
|
1.0
|
N
|
D:PHE86
|
4.6
|
38.4
|
1.0
|
CB
|
D:THR87
|
4.7
|
44.2
|
0.5
|
CB
|
E:ASP102
|
4.8
|
39.4
|
1.0
|
CD2
|
D:TYR95
|
4.8
|
35.6
|
1.0
|
CB
|
D:THR87
|
4.8
|
31.5
|
0.5
|
CA
|
D:SER84
|
5.0
|
34.7
|
0.2
|
|
Sodium binding site 8 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 8 out
of 10 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 8 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:Na319
b:71.5
occ:1.00
|
O
|
D:HOH500
|
2.3
|
69.8
|
1.0
|
O
|
C:HOH499
|
2.3
|
61.6
|
1.0
|
O
|
D:SER100
|
2.4
|
43.0
|
1.0
|
O
|
C:HOH466
|
2.6
|
40.7
|
1.0
|
O
|
D:HOH435
|
2.8
|
55.1
|
1.0
|
O
|
D:HOH478
|
2.9
|
62.6
|
1.0
|
C
|
D:SER100
|
3.6
|
44.1
|
1.0
|
NA
|
C:NA319
|
4.1
|
39.1
|
1.0
|
CA
|
D:GLY101
|
4.1
|
38.6
|
1.0
|
O
|
D:HOH498
|
4.1
|
67.0
|
1.0
|
N
|
D:GLY101
|
4.3
|
38.3
|
1.0
|
OD1
|
D:ASP102
|
4.3
|
38.2
|
1.0
|
C
|
D:GLY101
|
4.4
|
35.9
|
1.0
|
O
|
C:THR83
|
4.4
|
38.1
|
1.0
|
O
|
D:HOH425
|
4.6
|
35.9
|
1.0
|
O
|
C:HOH431
|
4.6
|
58.9
|
1.0
|
O
|
D:GLY101
|
4.7
|
43.4
|
1.0
|
CA
|
D:SER100
|
4.8
|
44.2
|
1.0
|
N
|
D:ASP102
|
4.8
|
35.3
|
1.0
|
O
|
D:HOH428
|
4.9
|
62.0
|
1.0
|
CG
|
D:ASP102
|
4.9
|
40.7
|
1.0
|
OG1
|
C:THR87
|
5.0
|
48.4
|
1.0
|
|
Sodium binding site 9 out
of 10 in 6yc3
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Sodium Binding Sites List in 6yc3
Sodium binding site 9 out
of 10 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 9 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:Na318
b:39.3
occ:1.00
|
O
|
E:THR83
|
2.2
|
39.0
|
1.0
|
O
|
E:HOH479
|
2.3
|
42.2
|
1.0
|
O
|
E:PHE86
|
2.4
|
38.0
|
1.0
|
OH
|
E:TYR25
|
2.4
|
37.1
|
1.0
|
OD1
|
A:ASP102
|
2.5
|
43.1
|
1.0
|
O
|
A:HOH451
|
2.7
|
59.3
|
1.0
|
CG
|
A:ASP102
|
3.2
|
39.8
|
1.0
|
OD2
|
A:ASP102
|
3.3
|
43.4
|
1.0
|
C
|
E:THR83
|
3.3
|
38.4
|
1.0
|
CZ
|
E:TYR25
|
3.4
|
38.3
|
1.0
|
C
|
E:PHE86
|
3.6
|
38.1
|
1.0
|
CA
|
E:THR83
|
3.8
|
36.9
|
1.0
|
O
|
A:HOH435
|
3.8
|
35.1
|
1.0
|
NA
|
A:NA322
|
3.8
|
78.6
|
1.0
|
CE1
|
E:TYR25
|
3.9
|
36.4
|
1.0
|
O
|
E:HOH517
|
4.1
|
67.0
|
1.0
|
CA
|
E:THR87
|
4.1
|
42.8
|
0.5
|
CA
|
E:THR87
|
4.2
|
37.3
|
0.5
|
CB
|
E:THR83
|
4.2
|
33.8
|
1.0
|
N
|
E:THR87
|
4.3
|
38.5
|
0.5
|
N
|
E:THR87
|
4.3
|
35.0
|
0.5
|
CG2
|
E:THR87
|
4.3
|
49.0
|
0.5
|
OG1
|
E:THR87
|
4.3
|
41.3
|
0.5
|
CE2
|
E:TYR25
|
4.4
|
36.0
|
1.0
|
N
|
E:SER84
|
4.5
|
36.0
|
0.2
|
N
|
E:SER84
|
4.5
|
34.0
|
0.2
|
N
|
E:SER84
|
4.5
|
36.3
|
0.5
|
CB
|
E:THR87
|
4.6
|
44.3
|
0.5
|
CA
|
E:PHE86
|
4.7
|
34.1
|
1.0
|
N
|
E:PHE86
|
4.7
|
37.0
|
1.0
|
CB
|
A:ASP102
|
4.7
|
40.3
|
1.0
|
CD2
|
E:TYR95
|
4.9
|
37.0
|
1.0
|
CB
|
E:THR87
|
4.9
|
35.5
|
0.5
|
O
|
E:HOH499
|
5.0
|
75.3
|
1.0
|
CA
|
E:SER84
|
5.0
|
35.6
|
0.2
|
CA
|
E:SER84
|
5.0
|
32.4
|
0.2
|
|
Sodium binding site 10 out
of 10 in 6yc3
Go back to
Sodium Binding Sites List in 6yc3
Sodium binding site 10 out
of 10 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 10 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:Na319
b:66.1
occ:1.00
|
O
|
E:HOH523
|
2.3
|
72.1
|
1.0
|
O
|
E:SER100
|
2.4
|
41.5
|
1.0
|
O
|
D:HOH474
|
2.5
|
62.0
|
1.0
|
O
|
E:HOH465
|
2.5
|
60.1
|
1.0
|
O
|
D:HOH469
|
2.6
|
39.4
|
1.0
|
O
|
E:HOH453
|
2.7
|
56.1
|
1.0
|
C
|
E:SER100
|
3.5
|
44.7
|
1.0
|
O
|
E:HOH510
|
4.0
|
71.8
|
1.0
|
CA
|
E:GLY101
|
4.0
|
41.8
|
1.0
|
O
|
E:HOH403
|
4.0
|
57.7
|
1.0
|
NA
|
D:NA318
|
4.1
|
38.8
|
1.0
|
N
|
E:GLY101
|
4.2
|
41.0
|
1.0
|
C
|
E:GLY101
|
4.3
|
39.6
|
1.0
|
OD1
|
E:ASP102
|
4.3
|
40.5
|
1.0
|
O
|
E:HOH426
|
4.4
|
39.4
|
1.0
|
O
|
D:THR83
|
4.5
|
39.3
|
1.0
|
O
|
E:GLY101
|
4.6
|
41.9
|
1.0
|
CA
|
E:SER100
|
4.7
|
42.7
|
1.0
|
N
|
E:ASP102
|
4.7
|
38.0
|
1.0
|
CG
|
E:ASP102
|
4.8
|
41.0
|
1.0
|
O
|
E:HOH519
|
4.9
|
75.6
|
1.0
|
O
|
D:HOH408
|
5.0
|
58.8
|
1.0
|
|
Reference:
K.Kovalev,
R.Astashkin,
I.Gushchin,
V.Gordeliy.
Molecular Mechanism of Light-Driven Sodium Pumping To Be Published.
Page generated: Tue Oct 8 15:02:41 2024
|