Sodium in PDB 6rez: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0
Protein crystallography data
The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0, PDB code: 6rez
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)
|
48.13 /
2.60
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
130.241,
241.392,
135.109,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
22.5
|
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 5.0
(pdb code 6rez). 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 5.0, PDB code: 6rez:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 6rez
Go back to
Sodium Binding Sites List in 6rez
Sodium binding site 1 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0
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 5.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na308
b:71.1
occ:1.00
|
O
|
A:HOH413
|
2.2
|
79.4
|
1.0
|
OH
|
A:TYR25
|
2.4
|
65.7
|
1.0
|
O
|
A:THR83
|
2.4
|
60.4
|
1.0
|
OD1
|
B:ASP102
|
2.4
|
95.8
|
1.0
|
O
|
A:PHE86
|
2.6
|
75.6
|
1.0
|
OD2
|
B:ASP102
|
3.1
|
72.7
|
1.0
|
CG
|
B:ASP102
|
3.1
|
79.5
|
1.0
|
CZ
|
A:TYR25
|
3.4
|
62.7
|
1.0
|
C
|
A:THR83
|
3.4
|
59.8
|
1.0
|
CA
|
A:THR83
|
3.8
|
58.9
|
1.0
|
C
|
A:PHE86
|
3.8
|
68.5
|
1.0
|
CE1
|
A:TYR25
|
4.0
|
61.2
|
1.0
|
CB
|
A:THR83
|
4.2
|
53.3
|
1.0
|
CE2
|
A:TYR25
|
4.3
|
61.3
|
1.0
|
CA
|
A:THR87
|
4.4
|
73.4
|
1.0
|
CB
|
B:ASP102
|
4.6
|
79.8
|
1.0
|
N
|
A:THR87
|
4.6
|
72.6
|
1.0
|
N
|
A:SER84
|
4.6
|
59.4
|
0.5
|
N
|
A:SER84
|
4.6
|
54.6
|
0.5
|
OG1
|
A:THR87
|
4.6
|
89.3
|
1.0
|
CD2
|
A:TYR95
|
4.8
|
56.6
|
1.0
|
CG2
|
A:THR83
|
4.8
|
54.9
|
1.0
|
CE2
|
A:TYR95
|
4.8
|
64.2
|
1.0
|
N
|
A:PHE86
|
4.9
|
62.4
|
1.0
|
CA
|
A:PHE86
|
5.0
|
65.3
|
1.0
|
|
Sodium binding site 2 out
of 5 in 6rez
Go back to
Sodium Binding Sites List in 6rez
Sodium binding site 2 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0
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 5.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na308
b:67.0
occ:1.00
|
O
|
B:HOH416
|
2.3
|
72.8
|
1.0
|
O
|
B:THR83
|
2.4
|
64.4
|
1.0
|
O
|
B:PHE86
|
2.4
|
62.0
|
1.0
|
OD1
|
C:ASP102
|
2.5
|
75.2
|
1.0
|
OH
|
B:TYR25
|
2.6
|
64.2
|
1.0
|
CG
|
C:ASP102
|
3.3
|
75.5
|
1.0
|
OD2
|
C:ASP102
|
3.4
|
70.5
|
1.0
|
O
|
C:HOH417
|
3.4
|
57.2
|
1.0
|
C
|
B:THR83
|
3.4
|
57.6
|
1.0
|
CZ
|
B:TYR25
|
3.5
|
64.6
|
1.0
|
C
|
B:PHE86
|
3.6
|
60.5
|
1.0
|
CA
|
B:THR83
|
3.9
|
59.8
|
1.0
|
CE1
|
B:TYR25
|
4.0
|
67.0
|
1.0
|
CA
|
B:THR87
|
4.2
|
77.1
|
1.0
|
CB
|
B:THR83
|
4.3
|
55.1
|
1.0
|
N
|
B:THR87
|
4.3
|
64.6
|
1.0
|
OG1
|
B:THR87
|
4.4
|
80.6
|
1.0
|
CE2
|
B:TYR25
|
4.4
|
64.0
|
1.0
|
N
|
B:SER84
|
4.6
|
55.6
|
0.5
|
N
|
B:SER84
|
4.6
|
62.3
|
0.5
|
CD2
|
B:TYR95
|
4.7
|
64.9
|
1.0
|
CB
|
C:ASP102
|
4.7
|
67.8
|
1.0
|
CA
|
B:PHE86
|
4.7
|
61.2
|
1.0
|
N
|
B:PHE86
|
4.8
|
63.1
|
1.0
|
CE2
|
B:TYR95
|
4.8
|
66.3
|
1.0
|
CB
|
B:THR87
|
4.9
|
65.8
|
1.0
|
O
|
C:SER100
|
4.9
|
0.3
|
1.0
|
|
Sodium binding site 3 out
of 5 in 6rez
Go back to
Sodium Binding Sites List in 6rez
Sodium binding site 3 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0
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 5.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na309
b:69.3
occ:1.00
|
O
|
C:HOH421
|
2.3
|
86.7
|
1.0
|
OH
|
C:TYR25
|
2.4
|
65.1
|
1.0
|
O
|
C:PHE86
|
2.4
|
68.9
|
1.0
|
O
|
C:THR83
|
2.4
|
58.9
|
1.0
|
OD1
|
D:ASP102
|
2.5
|
79.2
|
1.0
|
CG
|
D:ASP102
|
3.2
|
84.5
|
1.0
|
CZ
|
C:TYR25
|
3.3
|
63.2
|
1.0
|
OD2
|
D:ASP102
|
3.3
|
79.9
|
1.0
|
C
|
C:THR83
|
3.4
|
57.9
|
1.0
|
C
|
C:PHE86
|
3.6
|
68.0
|
1.0
|
O
|
C:HOH416
|
3.7
|
62.0
|
1.0
|
CE1
|
C:TYR25
|
3.8
|
60.9
|
1.0
|
CA
|
C:THR83
|
3.8
|
60.3
|
1.0
|
CE2
|
C:TYR25
|
4.2
|
56.1
|
1.0
|
CA
|
C:THR87
|
4.2
|
68.7
|
1.0
|
CB
|
C:THR83
|
4.2
|
56.0
|
1.0
|
N
|
C:THR87
|
4.4
|
67.4
|
1.0
|
OG1
|
C:THR87
|
4.5
|
85.4
|
1.0
|
CD2
|
C:TYR95
|
4.6
|
64.4
|
1.0
|
N
|
C:SER84
|
4.6
|
55.3
|
0.5
|
N
|
C:SER84
|
4.6
|
62.0
|
0.5
|
CE2
|
C:TYR95
|
4.7
|
73.2
|
1.0
|
CB
|
D:ASP102
|
4.7
|
69.0
|
1.0
|
CA
|
C:PHE86
|
4.7
|
64.1
|
1.0
|
N
|
C:PHE86
|
4.7
|
63.1
|
1.0
|
CG2
|
C:THR83
|
4.9
|
55.6
|
1.0
|
|
Sodium binding site 4 out
of 5 in 6rez
Go back to
Sodium Binding Sites List in 6rez
Sodium binding site 4 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0
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 5.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na307
b:71.4
occ:1.00
|
O
|
D:THR83
|
2.3
|
65.0
|
1.0
|
O
|
D:HOH403
|
2.4
|
89.3
|
1.0
|
OD1
|
E:ASP102
|
2.4
|
88.9
|
1.0
|
O
|
D:PHE86
|
2.5
|
69.0
|
1.0
|
OH
|
D:TYR25
|
2.7
|
62.5
|
1.0
|
CG
|
E:ASP102
|
3.2
|
74.2
|
1.0
|
OD2
|
E:ASP102
|
3.3
|
82.7
|
1.0
|
C
|
D:THR83
|
3.4
|
63.0
|
1.0
|
O
|
E:HOH413
|
3.6
|
63.9
|
1.0
|
CZ
|
D:TYR25
|
3.6
|
61.7
|
1.0
|
C
|
D:PHE86
|
3.7
|
59.0
|
1.0
|
CA
|
D:THR83
|
4.0
|
57.9
|
1.0
|
CE1
|
D:TYR25
|
4.2
|
65.0
|
1.0
|
CA
|
D:THR87
|
4.2
|
69.8
|
1.0
|
OG1
|
D:THR87
|
4.3
|
89.7
|
1.0
|
CB
|
D:THR83
|
4.4
|
57.3
|
1.0
|
N
|
D:THR87
|
4.4
|
63.4
|
1.0
|
CE2
|
D:TYR25
|
4.6
|
70.3
|
1.0
|
N
|
D:SER84
|
4.6
|
65.6
|
0.5
|
N
|
D:SER84
|
4.6
|
59.7
|
0.5
|
CB
|
E:ASP102
|
4.7
|
69.9
|
1.0
|
N
|
D:PHE86
|
4.8
|
58.2
|
1.0
|
CA
|
D:PHE86
|
4.8
|
59.8
|
1.0
|
O
|
E:SER100
|
4.8
|
96.6
|
1.0
|
CD2
|
D:TYR95
|
4.9
|
66.5
|
1.0
|
CB
|
D:THR87
|
4.9
|
71.2
|
1.0
|
CE2
|
D:TYR95
|
5.0
|
65.9
|
1.0
|
|
Sodium binding site 5 out
of 5 in 6rez
Go back to
Sodium Binding Sites List in 6rez
Sodium binding site 5 out
of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0
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 5.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na309
b:70.8
occ:1.00
|
O
|
E:THR83
|
2.4
|
72.5
|
1.0
|
OD1
|
A:ASP102
|
2.5
|
81.6
|
1.0
|
O
|
E:PHE86
|
2.6
|
67.1
|
1.0
|
OH
|
E:TYR25
|
2.6
|
65.2
|
1.0
|
CG
|
A:ASP102
|
3.3
|
73.4
|
1.0
|
OD2
|
A:ASP102
|
3.4
|
66.8
|
1.0
|
C
|
E:THR83
|
3.5
|
59.1
|
1.0
|
CZ
|
E:TYR25
|
3.6
|
58.9
|
1.0
|
C
|
E:PHE86
|
3.8
|
65.2
|
1.0
|
CA
|
E:THR83
|
4.0
|
63.3
|
1.0
|
CE1
|
E:TYR25
|
4.1
|
62.9
|
1.0
|
CA
|
E:THR87
|
4.3
|
73.6
|
1.0
|
CB
|
E:THR83
|
4.3
|
59.3
|
1.0
|
OG1
|
E:THR87
|
4.4
|
85.3
|
1.0
|
N
|
E:THR87
|
4.5
|
65.0
|
1.0
|
CE2
|
E:TYR25
|
4.5
|
57.0
|
1.0
|
N
|
E:SER84
|
4.6
|
57.9
|
0.5
|
N
|
E:SER84
|
4.6
|
62.8
|
0.5
|
CB
|
A:ASP102
|
4.7
|
77.7
|
1.0
|
CD2
|
E:TYR95
|
4.8
|
69.5
|
1.0
|
O
|
A:SER100
|
4.9
|
0.9
|
1.0
|
N
|
E:PHE86
|
4.9
|
52.7
|
1.0
|
CA
|
E:PHE86
|
4.9
|
62.7
|
1.0
|
CE2
|
E:TYR95
|
4.9
|
69.2
|
1.0
|
CB
|
E:THR87
|
5.0
|
72.8
|
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 13:07:33 2024
|