Sodium in PDB 3dj2: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Protein crystallography data
The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak, PDB code: 3dj2
was solved by
A.A.Serganov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.086,
78.751,
140.992,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.5 /
25.1
|
Other elements in 3dj2:
The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
(pdb code 3dj2). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak, PDB code: 3dj2:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 3dj2
Go back to
Sodium Binding Sites List in 3dj2
Sodium binding site 1 out
of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na201
b:36.0
occ:1.00
|
O
|
A:HOH315
|
2.4
|
22.6
|
1.0
|
O
|
A:HOH414
|
2.4
|
19.0
|
1.0
|
N7
|
A:G146
|
3.1
|
27.8
|
1.0
|
O
|
A:HOH415
|
3.6
|
21.4
|
1.0
|
O6
|
A:G146
|
3.6
|
27.9
|
1.0
|
N7
|
A:G147
|
3.7
|
26.7
|
1.0
|
N4
|
A:C145
|
3.8
|
26.1
|
1.0
|
C5
|
A:G146
|
3.9
|
28.0
|
1.0
|
O6
|
A:G147
|
3.9
|
27.1
|
1.0
|
C4
|
A:C145
|
4.0
|
26.1
|
1.0
|
C5
|
A:C145
|
4.0
|
26.1
|
1.0
|
C8
|
A:G146
|
4.1
|
27.8
|
1.0
|
C6
|
A:G146
|
4.1
|
27.9
|
1.0
|
C5
|
A:G147
|
4.5
|
27.2
|
1.0
|
C6
|
A:G147
|
4.5
|
27.1
|
1.0
|
N3
|
A:C145
|
4.7
|
26.3
|
1.0
|
C8
|
A:G147
|
4.8
|
26.9
|
1.0
|
C6
|
A:C145
|
4.8
|
26.2
|
1.0
|
|
Sodium binding site 2 out
of 8 in 3dj2
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Sodium Binding Sites List in 3dj2
Sodium binding site 2 out
of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:12.2
occ:1.00
|
O
|
A:HOH321
|
2.2
|
9.8
|
1.0
|
O6
|
A:G71
|
2.4
|
23.0
|
1.0
|
O
|
A:HOH344
|
2.5
|
10.8
|
1.0
|
O6
|
A:G20
|
2.6
|
21.3
|
1.0
|
O
|
A:HOH310
|
3.3
|
14.9
|
1.0
|
C6
|
A:G71
|
3.4
|
22.6
|
1.0
|
C6
|
A:G20
|
3.6
|
21.4
|
1.0
|
N7
|
A:G71
|
3.9
|
22.1
|
1.0
|
C5
|
A:G71
|
4.0
|
22.6
|
1.0
|
N7
|
A:G20
|
4.1
|
20.4
|
1.0
|
C5
|
A:G20
|
4.2
|
20.9
|
1.0
|
OP2
|
A:C70
|
4.4
|
22.5
|
1.0
|
OP2
|
A:C19
|
4.4
|
25.4
|
1.0
|
O
|
A:HOH311
|
4.5
|
11.9
|
1.0
|
N1
|
A:G71
|
4.6
|
22.2
|
1.0
|
N1
|
A:G20
|
4.8
|
21.3
|
1.0
|
|
Sodium binding site 3 out
of 8 in 3dj2
Go back to
Sodium Binding Sites List in 3dj2
Sodium binding site 3 out
of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na203
b:37.0
occ:1.00
|
O
|
A:HOH306
|
3.5
|
40.4
|
1.0
|
OP2
|
A:C130
|
4.0
|
27.7
|
1.0
|
OP1
|
A:A129
|
4.2
|
31.3
|
1.0
|
|
Sodium binding site 4 out
of 8 in 3dj2
Go back to
Sodium Binding Sites List in 3dj2
Sodium binding site 4 out
of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na204
b:21.4
occ:1.00
|
O
|
A:HOH351
|
2.5
|
18.8
|
1.0
|
OP2
|
A:G11
|
2.5
|
24.0
|
1.0
|
O
|
A:HOH352
|
2.6
|
21.2
|
1.0
|
O6
|
A:G12
|
2.7
|
25.3
|
1.0
|
P
|
A:G11
|
3.5
|
23.8
|
1.0
|
C6
|
A:G12
|
3.7
|
25.3
|
1.0
|
OP1
|
A:G11
|
3.8
|
24.4
|
1.0
|
N2
|
A:G11
|
4.1
|
23.1
|
1.0
|
O3'
|
A:A10
|
4.2
|
25.0
|
1.0
|
N4
|
A:C79
|
4.3
|
24.1
|
1.0
|
O
|
A:HOH329
|
4.3
|
8.3
|
1.0
|
OP1
|
A:A10
|
4.4
|
27.6
|
1.0
|
C5
|
A:G12
|
4.4
|
25.6
|
1.0
|
N7
|
A:G12
|
4.4
|
25.5
|
1.0
|
C3'
|
A:A10
|
4.7
|
26.0
|
1.0
|
N1
|
A:G12
|
4.7
|
24.7
|
1.0
|
O5'
|
A:A10
|
4.8
|
25.8
|
1.0
|
O5'
|
A:G11
|
4.9
|
23.9
|
1.0
|
P
|
A:A10
|
4.9
|
26.9
|
1.0
|
|
Sodium binding site 5 out
of 8 in 3dj2
Go back to
Sodium Binding Sites List in 3dj2
Sodium binding site 5 out
of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na205
b:27.1
occ:1.00
|
O
|
A:HOH330
|
2.6
|
6.2
|
1.0
|
OP1
|
A:C15
|
4.1
|
24.2
|
1.0
|
OP2
|
A:C132
|
4.2
|
24.1
|
1.0
|
OP1
|
A:G16
|
4.3
|
24.8
|
1.0
|
OP1
|
A:C131
|
4.5
|
25.6
|
1.0
|
OP1
|
A:G117
|
4.5
|
25.2
|
1.0
|
O
|
A:HOH380
|
4.5
|
15.5
|
1.0
|
OP1
|
A:C132
|
4.6
|
24.6
|
1.0
|
OP2
|
A:G16
|
4.7
|
24.5
|
1.0
|
OP2
|
A:G117
|
4.8
|
24.7
|
1.0
|
P
|
A:C132
|
4.9
|
25.3
|
1.0
|
P
|
A:G16
|
5.0
|
23.9
|
1.0
|
P
|
A:G117
|
5.0
|
25.4
|
1.0
|
|
Sodium binding site 6 out
of 8 in 3dj2
Go back to
Sodium Binding Sites List in 3dj2
Sodium binding site 6 out
of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na206
b:30.5
occ:1.00
|
O
|
A:HOH334
|
2.6
|
10.9
|
1.0
|
O6
|
A:G9
|
2.6
|
26.6
|
1.0
|
O
|
A:HOH417
|
2.9
|
20.1
|
1.0
|
C6
|
A:G9
|
3.6
|
26.2
|
1.0
|
N7
|
A:G9
|
3.7
|
25.6
|
1.0
|
C5
|
A:G9
|
4.0
|
25.7
|
1.0
|
O
|
A:HOH404
|
4.1
|
29.8
|
1.0
|
O6
|
A:G8
|
4.1
|
23.8
|
1.0
|
OP1
|
A:G80
|
4.2
|
22.4
|
1.0
|
O
|
A:HOH313
|
4.3
|
9.8
|
1.0
|
N4
|
A:C166
|
4.3
|
22.7
|
1.0
|
O
|
A:HOH305
|
4.6
|
14.9
|
1.0
|
C6
|
A:G8
|
4.9
|
23.7
|
1.0
|
N1
|
A:G9
|
4.9
|
26.1
|
1.0
|
C8
|
A:G9
|
4.9
|
26.1
|
1.0
|
N6
|
A:A10
|
4.9
|
26.7
|
1.0
|
O6
|
A:G165
|
5.0
|
25.4
|
1.0
|
|
Sodium binding site 7 out
of 8 in 3dj2
Go back to
Sodium Binding Sites List in 3dj2
Sodium binding site 7 out
of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na207
b:30.8
occ:1.00
|
O
|
A:HOH305
|
2.5
|
14.9
|
1.0
|
O
|
A:HOH417
|
3.0
|
20.1
|
1.0
|
OP2
|
A:G8
|
3.5
|
24.9
|
1.0
|
O
|
A:HOH403
|
3.5
|
15.8
|
1.0
|
OP1
|
A:C79
|
4.4
|
26.0
|
1.0
|
P
|
A:G8
|
4.6
|
25.4
|
1.0
|
O
|
A:HOH404
|
4.6
|
29.8
|
1.0
|
OP2
|
A:C79
|
4.8
|
26.7
|
1.0
|
OP1
|
A:G8
|
4.9
|
25.4
|
1.0
|
O5'
|
A:G8
|
5.0
|
24.7
|
1.0
|
|
Sodium binding site 8 out
of 8 in 3dj2
Go back to
Sodium Binding Sites List in 3dj2
Sodium binding site 8 out
of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na208
b:35.5
occ:1.00
|
O
|
A:HOH309
|
2.4
|
8.7
|
1.0
|
OP2
|
A:A133
|
4.1
|
25.0
|
1.0
|
OP2
|
A:G116
|
4.3
|
23.2
|
1.0
|
OP1
|
A:A133
|
4.4
|
26.6
|
1.0
|
OP1
|
A:G116
|
4.5
|
25.3
|
1.0
|
OP1
|
A:C132
|
4.5
|
24.6
|
1.0
|
O2'
|
A:G83
|
4.6
|
23.1
|
1.0
|
P
|
A:A133
|
4.8
|
25.2
|
1.0
|
P
|
A:G116
|
4.9
|
23.4
|
1.0
|
|
Reference:
A.Serganov,
L.Huang,
D.J.Patel.
Structural Insights Into Amino Acid Binding and Gene Control By A Lysine Riboswitch. Nature V. 455 1263 2008.
ISSN: ISSN 0028-0836
PubMed: 18784651
DOI: 10.1038/NATURE07326
Page generated: Mon Oct 7 08:33:54 2024
|