Sodium in PDB 6yc0: Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0
Protein crystallography data
The structure of Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0, PDB code: 6yc0
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)
|
50.01 /
2.70
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.210,
240.340,
138.370,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
19.2 /
22
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0
(pdb code 6yc0). 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0, PDB code: 6yc0:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 1 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na312
b:52.5
occ:1.00
|
O
|
A:PHE86
|
2.2
|
55.4
|
1.0
|
|
O
|
A:THR83
|
2.3
|
47.8
|
0.5
|
|
O
|
A:THR83
|
2.3
|
53.5
|
0.5
|
|
O
|
B:HOH446
|
2.4
|
75.8
|
1.0
|
|
OD1
|
B:ASP102
|
2.5
|
53.7
|
1.0
|
|
OH
|
A:TYR25
|
2.7
|
53.2
|
1.0
|
|
CG
|
B:ASP102
|
3.2
|
50.5
|
1.0
|
|
OD2
|
B:ASP102
|
3.2
|
47.8
|
1.0
|
|
C
|
A:PHE86
|
3.4
|
53.1
|
1.0
|
|
C
|
A:THR83
|
3.4
|
46.5
|
0.5
|
|
C
|
A:THR83
|
3.5
|
52.8
|
0.5
|
|
O
|
B:HOH414
|
3.6
|
38.7
|
1.0
|
|
CZ
|
A:TYR25
|
3.7
|
55.9
|
1.0
|
|
CA
|
A:THR83
|
4.0
|
49.5
|
0.5
|
|
CA
|
A:THR87
|
4.1
|
55.4
|
1.0
|
|
CA
|
A:THR83
|
4.1
|
57.4
|
0.5
|
|
N
|
A:THR87
|
4.1
|
54.6
|
1.0
|
|
CE1
|
A:TYR25
|
4.1
|
60.7
|
1.0
|
|
CA
|
A:PHE86
|
4.5
|
46.8
|
1.0
|
|
N
|
A:SER84
|
4.5
|
46.1
|
0.5
|
|
CB
|
A:THR83
|
4.5
|
46.0
|
0.5
|
|
OG1
|
A:THR87
|
4.6
|
62.6
|
1.0
|
|
N
|
A:SER84
|
4.6
|
51.5
|
0.5
|
|
N
|
A:PHE86
|
4.6
|
46.6
|
1.0
|
|
CB
|
A:THR83
|
4.6
|
54.2
|
0.5
|
|
CE2
|
A:TYR25
|
4.6
|
58.7
|
1.0
|
|
CB
|
B:ASP102
|
4.7
|
46.1
|
1.0
|
|
CD2
|
A:TYR95
|
4.8
|
47.4
|
1.0
|
|
O
|
B:SER100
|
4.9
|
82.2
|
1.0
|
|
CA
|
A:SER84
|
4.9
|
48.2
|
0.5
|
|
CB
|
A:THR87
|
4.9
|
51.0
|
1.0
|
|
CA
|
A:SER84
|
5.0
|
53.4
|
0.5
|
|
Sodium binding site 2 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 2 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na318
b:52.2
occ:0.50
|
OG
|
A:SER70
|
1.6
|
57.1
|
0.5
|
|
OD1
|
A:ASP116
|
1.7
|
65.0
|
0.5
|
|
CB
|
A:SER70
|
1.7
|
56.2
|
0.5
|
|
OD1
|
A:ASP116
|
1.8
|
59.6
|
0.5
|
|
OG
|
A:SER70
|
2.1
|
80.0
|
0.5
|
|
OD1
|
A:ASN112
|
2.3
|
39.4
|
0.5
|
|
CG
|
A:ASP116
|
2.5
|
64.3
|
0.5
|
|
OD2
|
A:ASP116
|
2.8
|
75.9
|
0.5
|
|
CG
|
A:ASP116
|
3.0
|
56.4
|
0.5
|
|
CA
|
A:SER70
|
3.0
|
49.4
|
0.5
|
|
CB
|
A:SER70
|
3.1
|
70.6
|
0.5
|
|
O
|
A:ASN112
|
3.2
|
66.8
|
0.5
|
|
C
|
A:SER70
|
3.4
|
44.2
|
0.5
|
|
O
|
A:VAL67
|
3.4
|
50.6
|
0.5
|
|
O
|
A:VAL67
|
3.4
|
52.0
|
0.5
|
|
N
|
A:ALA71
|
3.4
|
50.7
|
0.5
|
|
N
|
A:ALA71
|
3.5
|
41.8
|
0.5
|
|
OD2
|
A:ASP116
|
3.5
|
58.4
|
0.5
|
|
CG
|
A:ASN112
|
3.5
|
49.1
|
0.5
|
|
CG1
|
A:ILE115
|
3.6
|
78.4
|
0.5
|
|
CG2
|
A:ILE115
|
3.7
|
41.2
|
0.5
|
|
CD1
|
A:ILE115
|
3.7
|
79.1
|
0.5
|
|
C
|
A:SER70
|
3.8
|
58.2
|
0.5
|
|
O
|
A:ASN112
|
3.8
|
51.5
|
0.5
|
|
CB
|
A:ILE115
|
3.8
|
39.6
|
0.5
|
|
CB
|
A:ASP116
|
3.9
|
65.7
|
0.5
|
|
N
|
A:ASP116
|
3.9
|
41.6
|
0.5
|
|
N
|
A:SER70
|
3.9
|
42.1
|
0.5
|
|
O
|
A:HOH404
|
4.0
|
60.1
|
0.5
|
|
CA
|
A:SER70
|
4.0
|
59.6
|
0.5
|
|
CA
|
A:ALA71
|
4.0
|
53.1
|
0.5
|
|
O
|
A:SER70
|
4.1
|
46.1
|
0.5
|
|
CB
|
A:ASP116
|
4.2
|
51.8
|
0.5
|
|
C
|
A:ASN112
|
4.2
|
66.1
|
0.5
|
|
CA
|
A:ASP116
|
4.3
|
46.2
|
0.5
|
|
C
|
A:VAL67
|
4.3
|
54.9
|
0.5
|
|
C
|
A:VAL67
|
4.3
|
56.5
|
0.5
|
|
CB
|
A:ALA71
|
4.3
|
59.1
|
0.5
|
|
ND2
|
A:ASN112
|
4.3
|
54.2
|
0.5
|
|
CA
|
A:VAL67
|
4.3
|
58.5
|
0.5
|
|
CA
|
A:VAL67
|
4.3
|
57.6
|
0.5
|
|
N
|
A:ASP116
|
4.3
|
56.3
|
0.5
|
|
CA
|
A:ASN112
|
4.4
|
59.8
|
0.5
|
|
CA
|
A:ASP116
|
4.4
|
64.9
|
0.5
|
|
O
|
A:SER70
|
4.5
|
70.0
|
0.5
|
|
CA
|
A:ALA71
|
4.5
|
41.0
|
0.5
|
|
O
|
A:HOH401
|
4.5
|
64.4
|
0.5
|
|
CB
|
A:ASN112
|
4.5
|
58.0
|
0.5
|
|
CD1
|
A:ILE115
|
4.6
|
37.5
|
0.5
|
|
C
|
A:ILE115
|
4.6
|
39.7
|
0.5
|
|
O
|
A:HOH439
|
4.7
|
0.8
|
0.5
|
|
CG1
|
A:VAL67
|
4.7
|
52.4
|
0.5
|
|
CG1
|
A:VAL67
|
4.7
|
51.8
|
0.5
|
|
N
|
A:SER70
|
4.7
|
50.4
|
0.5
|
|
CG1
|
A:ILE115
|
4.7
|
37.9
|
0.5
|
|
CA
|
A:ILE115
|
4.8
|
41.3
|
0.5
|
|
C
|
A:ASN112
|
4.8
|
44.4
|
0.5
|
|
O
|
A:VAL66
|
4.9
|
53.5
|
1.0
|
|
C
|
A:ILE115
|
5.0
|
60.7
|
0.5
|
|
CB
|
A:ILE115
|
5.0
|
80.5
|
0.5
|
|
CB
|
A:ASN112
|
5.0
|
47.4
|
0.5
|
|
CB
|
A:ALA71
|
5.0
|
41.7
|
0.5
|
|
Sodium binding site 3 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 3 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na307
b:55.1
occ:1.00
|
O
|
B:HOH443
|
2.1
|
80.2
|
1.0
|
|
OD1
|
C:ASP102
|
2.3
|
63.0
|
1.0
|
|
O
|
B:THR83
|
2.3
|
49.5
|
0.5
|
|
O
|
B:THR83
|
2.4
|
57.1
|
0.5
|
|
O
|
B:PHE86
|
2.5
|
60.1
|
1.0
|
|
OH
|
B:TYR25
|
2.7
|
53.4
|
1.0
|
|
OD2
|
C:ASP102
|
2.9
|
68.0
|
1.0
|
|
CG
|
C:ASP102
|
2.9
|
57.1
|
1.0
|
|
C
|
B:THR83
|
3.5
|
41.2
|
0.5
|
|
O
|
C:HOH413
|
3.6
|
37.2
|
1.0
|
|
C
|
B:THR83
|
3.6
|
50.2
|
0.5
|
|
C
|
B:PHE86
|
3.6
|
50.3
|
1.0
|
|
CZ
|
B:TYR25
|
3.6
|
46.1
|
1.0
|
|
CA
|
B:THR83
|
4.0
|
42.8
|
0.5
|
|
CA
|
B:THR83
|
4.2
|
54.1
|
0.5
|
|
CE1
|
B:TYR25
|
4.2
|
59.0
|
1.0
|
|
CA
|
B:THR87
|
4.2
|
52.5
|
1.0
|
|
N
|
B:THR87
|
4.3
|
51.6
|
1.0
|
|
CB
|
C:ASP102
|
4.4
|
51.3
|
1.0
|
|
CB
|
B:THR83
|
4.5
|
45.4
|
0.5
|
|
CE2
|
B:TYR25
|
4.6
|
49.0
|
1.0
|
|
CB
|
B:THR83
|
4.6
|
57.4
|
0.5
|
|
N
|
B:SER84
|
4.6
|
42.0
|
0.5
|
|
OG1
|
B:THR87
|
4.7
|
51.7
|
1.0
|
|
O
|
C:SER100
|
4.7
|
68.0
|
1.0
|
|
N
|
B:SER84
|
4.7
|
51.2
|
0.5
|
|
CA
|
B:PHE86
|
4.8
|
47.4
|
1.0
|
|
CD2
|
B:TYR95
|
4.9
|
58.7
|
1.0
|
|
N
|
B:PHE86
|
4.9
|
43.8
|
1.0
|
|
CE2
|
B:TYR95
|
5.0
|
64.7
|
1.0
|
|
Sodium binding site 4 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 4 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na312
b:81.7
occ:0.50
|
OD1
|
B:ASN112
|
1.6
|
46.6
|
0.5
|
|
OG
|
B:SER70
|
1.6
|
58.9
|
0.5
|
|
CB
|
B:SER70
|
1.9
|
51.3
|
0.5
|
|
OD1
|
B:ASP116
|
2.0
|
65.9
|
0.5
|
|
OD1
|
B:ASP116
|
2.2
|
51.9
|
0.5
|
|
OG
|
B:SER70
|
2.4
|
57.1
|
0.5
|
|
OD2
|
B:ASP116
|
2.6
|
69.7
|
0.5
|
|
CG
|
B:ASP116
|
2.7
|
65.1
|
0.5
|
|
CG
|
B:ASN112
|
2.7
|
57.7
|
0.5
|
|
CG
|
B:ASP116
|
2.9
|
66.0
|
0.5
|
|
N
|
B:ALA71
|
2.9
|
52.7
|
0.5
|
|
CA
|
B:SER70
|
2.9
|
48.0
|
0.5
|
|
C
|
B:SER70
|
2.9
|
46.3
|
0.5
|
|
N
|
B:ALA71
|
3.1
|
47.4
|
0.5
|
|
OD2
|
B:ASP116
|
3.1
|
60.0
|
0.5
|
|
CB
|
B:SER70
|
3.2
|
56.3
|
0.5
|
|
O
|
B:ASN112
|
3.2
|
79.3
|
0.5
|
|
O
|
B:HOH402
|
3.4
|
50.3
|
0.5
|
|
C
|
B:SER70
|
3.4
|
49.6
|
0.5
|
|
ND2
|
B:ASN112
|
3.5
|
64.2
|
0.5
|
|
CA
|
B:ALA71
|
3.5
|
47.6
|
0.5
|
|
O
|
B:VAL67
|
3.5
|
44.4
|
0.5
|
|
O
|
B:VAL67
|
3.5
|
44.2
|
0.5
|
|
O
|
B:SER70
|
3.6
|
44.7
|
0.5
|
|
O
|
B:HOH405
|
3.7
|
71.9
|
0.5
|
|
CA
|
B:ALA71
|
3.8
|
48.1
|
0.5
|
|
O
|
B:ASN112
|
3.8
|
56.4
|
0.5
|
|
CB
|
B:ALA71
|
3.9
|
48.5
|
0.5
|
|
CB
|
B:ASN112
|
3.9
|
69.4
|
0.5
|
|
N
|
B:SER70
|
3.9
|
42.0
|
0.5
|
|
CA
|
B:SER70
|
3.9
|
54.7
|
0.5
|
|
C
|
B:ASN112
|
4.0
|
74.2
|
0.5
|
|
CA
|
B:ASN112
|
4.0
|
72.8
|
0.5
|
|
O
|
B:SER70
|
4.0
|
55.5
|
0.5
|
|
CG1
|
B:ILE115
|
4.1
|
64.2
|
0.5
|
|
CD1
|
B:ILE115
|
4.1
|
66.4
|
0.5
|
|
CB
|
B:ASP116
|
4.2
|
60.7
|
0.5
|
|
CB
|
B:ASP116
|
4.2
|
58.4
|
0.5
|
|
CG2
|
B:ILE115
|
4.3
|
45.6
|
0.5
|
|
N
|
B:ASP116
|
4.3
|
50.8
|
0.5
|
|
CB
|
B:ILE115
|
4.3
|
46.4
|
0.5
|
|
CB
|
B:ALA71
|
4.4
|
46.5
|
0.5
|
|
C
|
B:VAL67
|
4.5
|
47.3
|
0.5
|
|
C
|
B:VAL67
|
4.5
|
47.0
|
0.5
|
|
CA
|
B:ASP116
|
4.6
|
53.8
|
0.5
|
|
CB
|
B:ASN112
|
4.6
|
61.1
|
0.5
|
|
ND2
|
B:ASN112
|
4.7
|
53.1
|
0.5
|
|
N
|
B:SER70
|
4.7
|
52.2
|
0.5
|
|
C
|
B:ASN112
|
4.7
|
56.1
|
0.5
|
|
O
|
B:HOH408
|
4.8
|
0.4
|
1.0
|
|
CA
|
B:VAL67
|
4.8
|
55.4
|
0.5
|
|
CA
|
B:VAL67
|
4.8
|
55.2
|
0.5
|
|
N
|
B:ASP116
|
4.8
|
54.4
|
0.5
|
|
CD2
|
B:LEU74
|
4.8
|
61.5
|
0.5
|
|
CA
|
B:ASP116
|
4.8
|
56.5
|
0.5
|
|
CG1
|
B:VAL67
|
4.9
|
55.3
|
0.5
|
|
C
|
B:ALA71
|
4.9
|
43.2
|
0.5
|
|
CG1
|
B:VAL67
|
4.9
|
55.4
|
0.5
|
|
Sodium binding site 5 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 5 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na311
b:49.8
occ:1.00
|
O
|
C:THR83
|
2.3
|
54.4
|
0.5
|
|
O
|
C:PHE86
|
2.3
|
55.1
|
1.0
|
|
O
|
D:HOH436
|
2.3
|
72.0
|
1.0
|
|
OD1
|
D:ASP102
|
2.4
|
57.7
|
1.0
|
|
O
|
C:THR83
|
2.4
|
54.6
|
0.5
|
|
OH
|
C:TYR25
|
2.5
|
43.9
|
1.0
|
|
OD2
|
D:ASP102
|
3.0
|
48.0
|
1.0
|
|
CG
|
D:ASP102
|
3.0
|
53.5
|
1.0
|
|
O
|
D:HOH425
|
3.1
|
61.9
|
1.0
|
|
C
|
C:THR83
|
3.4
|
48.0
|
0.5
|
|
CZ
|
C:TYR25
|
3.5
|
48.1
|
1.0
|
|
C
|
C:THR83
|
3.5
|
50.2
|
0.5
|
|
C
|
C:PHE86
|
3.5
|
49.5
|
1.0
|
|
O
|
D:HOH420
|
3.7
|
40.0
|
1.0
|
|
CA
|
C:THR83
|
3.9
|
47.7
|
0.5
|
|
CE1
|
C:TYR25
|
4.0
|
58.1
|
1.0
|
|
CA
|
C:THR83
|
4.0
|
52.6
|
0.5
|
|
CA
|
C:THR87
|
4.2
|
52.6
|
1.0
|
|
N
|
C:THR87
|
4.3
|
48.9
|
1.0
|
|
CB
|
C:THR83
|
4.4
|
51.2
|
0.5
|
|
CE2
|
C:TYR25
|
4.4
|
61.2
|
1.0
|
|
CB
|
D:ASP102
|
4.5
|
51.4
|
1.0
|
|
CB
|
C:THR83
|
4.5
|
58.0
|
0.5
|
|
N
|
C:SER84
|
4.6
|
51.7
|
0.5
|
|
CA
|
C:PHE86
|
4.6
|
51.0
|
1.0
|
|
N
|
C:SER84
|
4.7
|
54.5
|
0.5
|
|
OG1
|
C:THR87
|
4.7
|
62.7
|
1.0
|
|
CD2
|
C:TYR95
|
4.8
|
53.4
|
1.0
|
|
N
|
C:PHE86
|
4.8
|
50.0
|
1.0
|
|
CE2
|
C:TYR95
|
4.9
|
62.4
|
1.0
|
|
O
|
D:SER100
|
5.0
|
86.2
|
1.0
|
|
Sodium binding site 6 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 6 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na316
b:71.3
occ:0.50
|
OG
|
C:SER70
|
1.5
|
57.6
|
0.5
|
|
OD1
|
C:ASN112
|
1.7
|
45.4
|
0.5
|
|
CB
|
C:SER70
|
1.9
|
55.6
|
0.5
|
|
OD1
|
C:ASP116
|
1.9
|
64.2
|
0.5
|
|
OD1
|
C:ASP116
|
2.0
|
63.7
|
0.5
|
|
OG
|
C:SER70
|
2.4
|
59.2
|
0.5
|
|
CG
|
C:ASP116
|
2.6
|
69.6
|
0.5
|
|
OD2
|
C:ASP116
|
2.6
|
69.8
|
0.5
|
|
CG
|
C:ASP116
|
2.9
|
64.2
|
0.5
|
|
CG
|
C:ASN112
|
2.9
|
51.6
|
0.5
|
|
CA
|
C:SER70
|
2.9
|
51.2
|
0.5
|
|
C
|
C:SER70
|
3.0
|
49.6
|
0.5
|
|
N
|
C:ALA71
|
3.0
|
46.7
|
0.5
|
|
O
|
C:ASN112
|
3.1
|
71.7
|
0.5
|
|
N
|
C:ALA71
|
3.2
|
50.5
|
0.5
|
|
OD2
|
C:ASP116
|
3.2
|
62.7
|
0.5
|
|
CB
|
C:SER70
|
3.2
|
64.2
|
0.5
|
|
C
|
C:SER70
|
3.5
|
56.8
|
0.5
|
|
O
|
C:VAL67
|
3.5
|
53.8
|
0.5
|
|
O
|
C:VAL67
|
3.6
|
53.6
|
0.5
|
|
CA
|
C:ALA71
|
3.6
|
46.7
|
0.5
|
|
ND2
|
C:ASN112
|
3.7
|
52.5
|
0.5
|
|
O
|
C:SER70
|
3.7
|
49.3
|
0.5
|
|
O
|
C:ASN112
|
3.8
|
37.3
|
0.5
|
|
CG1
|
C:ILE115
|
3.8
|
74.7
|
0.5
|
|
CD1
|
C:ILE115
|
3.9
|
71.1
|
0.5
|
|
C
|
C:ASN112
|
3.9
|
70.2
|
0.5
|
|
N
|
C:SER70
|
3.9
|
48.7
|
0.5
|
|
CA
|
C:SER70
|
3.9
|
58.9
|
0.5
|
|
CA
|
C:ASN112
|
4.0
|
65.3
|
0.5
|
|
CA
|
C:ALA71
|
4.0
|
40.0
|
0.5
|
|
O
|
C:HOH402
|
4.0
|
61.6
|
0.5
|
|
CB
|
C:ASN112
|
4.0
|
61.1
|
0.5
|
|
CB
|
C:ALA71
|
4.0
|
46.1
|
0.5
|
|
CB
|
C:ASP116
|
4.1
|
62.5
|
0.5
|
|
CB
|
C:ILE115
|
4.1
|
40.7
|
0.5
|
|
CG2
|
C:ILE115
|
4.1
|
38.2
|
0.5
|
|
O
|
C:SER70
|
4.2
|
65.4
|
0.5
|
|
N
|
C:ASP116
|
4.2
|
43.1
|
0.5
|
|
CB
|
C:ASP116
|
4.2
|
52.0
|
0.5
|
|
CA
|
C:ASP116
|
4.5
|
44.7
|
0.5
|
|
CB
|
C:ASN112
|
4.6
|
42.1
|
0.5
|
|
C
|
C:VAL67
|
4.6
|
51.9
|
0.5
|
|
C
|
C:VAL67
|
4.6
|
52.0
|
0.5
|
|
CB
|
C:ALA71
|
4.6
|
38.5
|
0.5
|
|
N
|
C:ASP116
|
4.6
|
60.0
|
0.5
|
|
C
|
C:ASN112
|
4.6
|
40.3
|
0.5
|
|
ND2
|
C:ASN112
|
4.6
|
48.5
|
0.5
|
|
O
|
C:HOH443
|
4.7
|
56.4
|
0.5
|
|
CA
|
C:ASP116
|
4.7
|
57.7
|
0.5
|
|
CA
|
C:VAL67
|
4.8
|
56.6
|
0.5
|
|
CA
|
C:VAL67
|
4.8
|
56.8
|
0.5
|
|
N
|
C:SER70
|
4.8
|
59.2
|
0.5
|
|
CD1
|
C:ILE115
|
4.8
|
39.9
|
0.5
|
|
CD2
|
C:LEU74
|
4.9
|
67.0
|
0.5
|
|
O
|
C:HOH444
|
4.9
|
0.3
|
0.5
|
|
C
|
C:ILE115
|
4.9
|
41.9
|
0.5
|
|
CG1
|
C:VAL67
|
5.0
|
52.1
|
0.5
|
|
CG1
|
C:VAL67
|
5.0
|
52.1
|
0.5
|
|
Sodium binding site 7 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 7 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na310
b:46.3
occ:1.00
|
O
|
D:PHE86
|
2.2
|
60.5
|
1.0
|
|
O
|
D:THR83
|
2.3
|
55.8
|
0.5
|
|
O
|
D:THR83
|
2.3
|
59.1
|
0.5
|
|
O
|
D:HOH437
|
2.4
|
61.7
|
1.0
|
|
OD1
|
E:ASP102
|
2.4
|
73.6
|
1.0
|
|
OH
|
D:TYR25
|
2.5
|
49.0
|
1.0
|
|
OD2
|
E:ASP102
|
3.0
|
63.8
|
1.0
|
|
CG
|
E:ASP102
|
3.1
|
63.5
|
1.0
|
|
C
|
D:THR83
|
3.3
|
48.7
|
0.5
|
|
CZ
|
D:TYR25
|
3.4
|
48.1
|
1.0
|
|
C
|
D:PHE86
|
3.4
|
52.2
|
1.0
|
|
C
|
D:THR83
|
3.5
|
55.0
|
0.5
|
|
CA
|
D:THR83
|
3.8
|
49.7
|
0.5
|
|
O
|
E:HOH519
|
3.8
|
39.7
|
1.0
|
|
CE1
|
D:TYR25
|
3.8
|
51.0
|
1.0
|
|
CA
|
D:THR83
|
4.0
|
57.7
|
0.5
|
|
CA
|
D:THR87
|
4.2
|
53.1
|
1.0
|
|
N
|
D:THR87
|
4.2
|
51.4
|
1.0
|
|
CB
|
D:THR83
|
4.3
|
50.1
|
0.5
|
|
CE2
|
D:TYR25
|
4.4
|
49.7
|
1.0
|
|
CB
|
D:THR83
|
4.5
|
58.3
|
0.5
|
|
CA
|
D:PHE86
|
4.5
|
50.4
|
1.0
|
|
N
|
D:SER84
|
4.5
|
50.8
|
0.5
|
|
CB
|
E:ASP102
|
4.5
|
51.6
|
1.0
|
|
N
|
D:SER84
|
4.6
|
57.9
|
0.5
|
|
N
|
D:PHE86
|
4.6
|
49.0
|
1.0
|
|
CD2
|
D:TYR95
|
4.7
|
56.5
|
1.0
|
|
OG1
|
D:THR87
|
4.7
|
59.0
|
1.0
|
|
CE2
|
D:TYR95
|
4.8
|
52.7
|
1.0
|
|
CB
|
D:PHE86
|
5.0
|
48.0
|
1.0
|
|
Sodium binding site 8 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 8 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na314
b:48.2
occ:0.50
|
OG
|
D:SER70
|
1.4
|
64.9
|
0.5
|
|
OD1
|
D:ASN112
|
1.8
|
30.4
|
0.5
|
|
CB
|
D:SER70
|
1.8
|
59.2
|
0.5
|
|
OD1
|
D:ASP116
|
2.1
|
59.4
|
0.5
|
|
OD1
|
D:ASP116
|
2.1
|
62.1
|
0.5
|
|
OG
|
D:SER70
|
2.4
|
53.3
|
0.5
|
|
OD2
|
D:ASP116
|
2.7
|
67.4
|
0.5
|
|
CG
|
D:ASP116
|
2.7
|
64.2
|
0.5
|
|
CG
|
D:ASP116
|
2.7
|
60.7
|
0.5
|
|
CA
|
D:SER70
|
2.8
|
56.0
|
0.5
|
|
OD2
|
D:ASP116
|
2.8
|
57.1
|
0.5
|
|
C
|
D:SER70
|
2.8
|
50.4
|
0.5
|
|
CG2
|
D:ILE115
|
2.9
|
59.7
|
0.5
|
|
CG
|
D:ASN112
|
2.9
|
43.2
|
0.5
|
|
N
|
D:ALA71
|
3.0
|
53.6
|
0.5
|
|
N
|
D:ALA71
|
3.1
|
44.0
|
0.5
|
|
CB
|
D:SER70
|
3.2
|
57.9
|
0.5
|
|
O
|
D:ASN112
|
3.2
|
63.5
|
0.5
|
|
O
|
D:HOH401
|
3.4
|
43.0
|
0.5
|
|
O
|
D:ASN112
|
3.4
|
63.0
|
0.5
|
|
C
|
D:SER70
|
3.5
|
45.5
|
0.5
|
|
O
|
D:SER70
|
3.5
|
56.7
|
0.5
|
|
CA
|
D:ALA71
|
3.5
|
47.9
|
0.5
|
|
O
|
D:VAL67
|
3.6
|
57.1
|
0.5
|
|
O
|
D:VAL67
|
3.7
|
58.5
|
0.5
|
|
ND2
|
D:ASN112
|
3.7
|
46.2
|
0.5
|
|
N
|
D:SER70
|
3.9
|
50.9
|
0.5
|
|
CA
|
D:SER70
|
3.9
|
53.0
|
0.5
|
|
CG1
|
D:ILE115
|
3.9
|
47.4
|
0.5
|
|
CA
|
D:ALA71
|
3.9
|
47.6
|
0.5
|
|
ND2
|
D:ASN112
|
4.0
|
53.0
|
0.5
|
|
CB
|
D:ALA71
|
4.0
|
46.5
|
0.5
|
|
CD1
|
D:ILE115
|
4.0
|
45.6
|
0.5
|
|
C
|
D:ASN112
|
4.0
|
58.3
|
0.5
|
|
CB
|
D:ASN112
|
4.1
|
52.5
|
0.5
|
|
CB
|
D:ASN112
|
4.1
|
57.8
|
0.5
|
|
CA
|
D:ASN112
|
4.1
|
57.5
|
0.5
|
|
CB
|
D:ASP116
|
4.1
|
58.5
|
0.5
|
|
CB
|
D:ASP116
|
4.1
|
60.6
|
0.5
|
|
O
|
D:SER70
|
4.2
|
53.2
|
0.5
|
|
O
|
D:HOH404
|
4.2
|
22.1
|
0.5
|
|
C
|
D:ASN112
|
4.4
|
54.6
|
0.5
|
|
CB
|
D:ILE115
|
4.4
|
57.2
|
0.5
|
|
N
|
D:ASP116
|
4.5
|
51.4
|
0.5
|
|
CG
|
D:ASN112
|
4.5
|
54.6
|
0.5
|
|
CB
|
D:ALA71
|
4.6
|
38.1
|
0.5
|
|
CA
|
D:ASP116
|
4.6
|
56.0
|
0.5
|
|
C
|
D:VAL67
|
4.7
|
52.5
|
0.5
|
|
C
|
D:VAL67
|
4.7
|
53.2
|
0.5
|
|
CD2
|
D:LEU74
|
4.7
|
60.6
|
0.5
|
|
N
|
D:ASP116
|
4.7
|
45.5
|
0.5
|
|
CA
|
D:ASN112
|
4.7
|
55.0
|
0.5
|
|
C
|
D:ILE115
|
4.7
|
51.2
|
0.5
|
|
CA
|
D:ASP116
|
4.8
|
54.6
|
0.5
|
|
N
|
D:SER70
|
4.8
|
51.3
|
0.5
|
|
CA
|
D:VAL67
|
4.9
|
56.2
|
0.5
|
|
CA
|
D:VAL67
|
4.9
|
56.9
|
0.5
|
|
C
|
D:ALA71
|
5.0
|
47.1
|
0.5
|
|
O
|
D:HOH441
|
5.0
|
0.3
|
0.5
|
|
Sodium binding site 9 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 9 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na412
b:36.2
occ:1.00
|
O
|
E:HOH537
|
2.3
|
64.6
|
1.0
|
|
O
|
E:PHE86
|
2.3
|
54.0
|
1.0
|
|
OD1
|
A:ASP102
|
2.4
|
62.8
|
1.0
|
|
O
|
E:THR83
|
2.4
|
60.5
|
0.5
|
|
O
|
E:THR83
|
2.5
|
59.2
|
0.5
|
|
OH
|
E:TYR25
|
2.6
|
46.5
|
1.0
|
|
OD2
|
A:ASP102
|
3.0
|
55.8
|
1.0
|
|
CG
|
A:ASP102
|
3.0
|
55.8
|
1.0
|
|
O
|
A:HOH409
|
3.4
|
39.8
|
1.0
|
|
C
|
E:THR83
|
3.5
|
50.3
|
0.5
|
|
CZ
|
E:TYR25
|
3.5
|
45.6
|
1.0
|
|
C
|
E:PHE86
|
3.5
|
44.5
|
1.0
|
|
C
|
E:THR83
|
3.6
|
53.5
|
0.5
|
|
CA
|
E:THR83
|
3.9
|
47.0
|
0.5
|
|
CE1
|
E:TYR25
|
4.0
|
53.5
|
1.0
|
|
CA
|
E:THR83
|
4.1
|
52.0
|
0.5
|
|
CA
|
E:THR87
|
4.2
|
51.5
|
1.0
|
|
N
|
E:THR87
|
4.2
|
44.8
|
1.0
|
|
CB
|
E:THR83
|
4.4
|
48.0
|
0.5
|
|
CE2
|
E:TYR25
|
4.5
|
50.7
|
1.0
|
|
CB
|
A:ASP102
|
4.5
|
45.2
|
1.0
|
|
N
|
E:SER84
|
4.6
|
47.4
|
0.5
|
|
CB
|
E:THR83
|
4.6
|
53.6
|
0.5
|
|
CA
|
E:PHE86
|
4.7
|
49.7
|
1.0
|
|
OG1
|
E:THR87
|
4.7
|
52.7
|
1.0
|
|
N
|
E:SER84
|
4.7
|
50.0
|
0.5
|
|
CD2
|
E:TYR95
|
4.7
|
60.2
|
1.0
|
|
N
|
E:PHE86
|
4.8
|
46.9
|
1.0
|
|
CE2
|
E:TYR95
|
4.9
|
55.2
|
1.0
|
|
O
|
A:SER100
|
4.9
|
72.7
|
1.0
|
|
Sodium binding site 10 out
of 10 in 6yc0
Go back to
Sodium Binding Sites List in 6yc0
Sodium binding site 10 out
of 10 in the Crystal Structure of the Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Steady-State-Smx Activated State of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na415
b:57.0
occ:0.50
|
CB
|
E:SER70
|
1.5
|
50.1
|
0.5
|
|
OG
|
E:SER70
|
1.6
|
44.5
|
0.5
|
|
OD1
|
E:ASN112
|
1.9
|
49.4
|
0.5
|
|
OD1
|
E:ASP116
|
2.0
|
66.0
|
0.5
|
|
OD1
|
E:ASP116
|
2.2
|
61.5
|
0.5
|
|
OG
|
E:SER70
|
2.2
|
74.8
|
0.5
|
|
CA
|
E:SER70
|
2.5
|
47.6
|
0.5
|
|
C
|
E:SER70
|
2.7
|
43.9
|
0.5
|
|
OD2
|
E:ASP116
|
2.8
|
64.5
|
0.5
|
|
N
|
E:ALA71
|
2.8
|
42.3
|
0.5
|
|
CG
|
E:ASP116
|
2.8
|
61.0
|
0.5
|
|
N
|
E:ALA71
|
2.9
|
46.8
|
0.5
|
|
CG
|
E:ASP116
|
3.1
|
54.6
|
0.5
|
|
CB
|
E:SER70
|
3.1
|
65.0
|
0.5
|
|
CG
|
E:ASN112
|
3.1
|
59.4
|
0.5
|
|
O
|
E:VAL67
|
3.2
|
57.4
|
0.5
|
|
O
|
E:VAL67
|
3.2
|
62.5
|
0.5
|
|
O
|
E:HOH502
|
3.2
|
49.8
|
0.5
|
|
C
|
E:SER70
|
3.3
|
52.9
|
0.5
|
|
CA
|
E:ALA71
|
3.4
|
50.9
|
0.5
|
|
O
|
E:SER70
|
3.5
|
44.5
|
0.5
|
|
N
|
E:SER70
|
3.5
|
41.3
|
0.5
|
|
OD2
|
E:ASP116
|
3.5
|
49.7
|
0.5
|
|
O
|
E:ASN112
|
3.5
|
72.5
|
0.5
|
|
CB
|
E:ALA71
|
3.7
|
58.0
|
0.5
|
|
CA
|
E:SER70
|
3.7
|
55.5
|
0.5
|
|
CA
|
E:ALA71
|
3.8
|
42.7
|
0.5
|
|
ND2
|
E:ASN112
|
3.9
|
61.7
|
0.5
|
|
O
|
E:SER70
|
3.9
|
56.2
|
0.5
|
|
CD1
|
E:ILE115
|
3.9
|
67.7
|
0.5
|
|
CG1
|
E:ILE115
|
4.0
|
64.9
|
0.5
|
|
O
|
E:ASN112
|
4.1
|
37.6
|
0.5
|
|
CG2
|
E:ILE115
|
4.1
|
42.1
|
0.5
|
|
C
|
E:VAL67
|
4.2
|
55.5
|
0.5
|
|
C
|
E:VAL67
|
4.2
|
58.1
|
0.5
|
|
CB
|
E:ASP116
|
4.2
|
56.9
|
0.5
|
|
CB
|
E:ASN112
|
4.3
|
66.0
|
0.5
|
|
CA
|
E:ASN112
|
4.3
|
69.5
|
0.5
|
|
C
|
E:ASN112
|
4.3
|
68.6
|
0.5
|
|
CB
|
E:ILE115
|
4.3
|
41.9
|
0.5
|
|
N
|
E:ASP116
|
4.4
|
41.1
|
0.5
|
|
CB
|
E:ALA71
|
4.4
|
44.7
|
0.5
|
|
CB
|
E:ASP116
|
4.4
|
49.5
|
0.5
|
|
CA
|
E:VAL67
|
4.4
|
63.0
|
0.5
|
|
CA
|
E:VAL67
|
4.4
|
60.5
|
0.5
|
|
N
|
E:SER70
|
4.5
|
49.6
|
0.5
|
|
O
|
E:HOH540
|
4.5
|
67.2
|
0.5
|
|
CA
|
E:ASP116
|
4.7
|
45.0
|
0.5
|
|
O
|
E:HOH525
|
4.7
|
85.7
|
0.5
|
|
CG1
|
E:VAL67
|
4.7
|
61.1
|
0.5
|
|
C
|
E:VAL69
|
4.7
|
41.4
|
0.5
|
|
CG1
|
E:VAL67
|
4.7
|
57.8
|
0.5
|
|
N
|
E:ASP116
|
4.8
|
48.7
|
0.5
|
|
C
|
E:ALA71
|
4.8
|
51.5
|
0.5
|
|
ND2
|
E:ASN112
|
4.8
|
51.7
|
0.5
|
|
CA
|
E:ASP116
|
4.8
|
50.7
|
0.5
|
|
CB
|
E:ASN112
|
4.8
|
45.2
|
0.5
|
|
CD2
|
E:LEU74
|
4.9
|
57.6
|
0.5
|
|
CD1
|
E:ILE115
|
4.9
|
39.7
|
0.5
|
|
C
|
E:ASN112
|
5.0
|
40.6
|
0.5
|
|
Reference:
K.Kovalev,
R.Astashkin,
I.Gushchin,
V.Gordeliy.
Molecular Mechanism of Light-Driven Sodium Pumping To Be Published.
Page generated: Tue Oct 8 15:02:21 2024
|
