Cobalt in PDB 6uc8: Guanine Riboswitch Bound to 8-Aminoguanine
Protein crystallography data
The structure of Guanine Riboswitch Bound to 8-Aminoguanine, PDB code: 6uc8
was solved by
M.M.Matyjasik,
S.D.Hall,
R.T.Batey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.96 /
1.90
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
132.545,
35.184,
41.934,
90.00,
90.34,
90.00
|
R / Rfree (%)
|
18.7 /
22.4
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Guanine Riboswitch Bound to 8-Aminoguanine
(pdb code 6uc8). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the
Guanine Riboswitch Bound to 8-Aminoguanine, PDB code: 6uc8:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Cobalt binding site 1 out
of 8 in 6uc8
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Cobalt Binding Sites List in 6uc8
Cobalt binding site 1 out
of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_01.jpg) Mono view
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Guanine Riboswitch Bound to 8-Aminoguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co102
b:52.2
occ:1.00
|
CO
|
B:NCO102
|
0.0
|
52.2
|
1.0
|
N1
|
B:NCO102
|
2.0
|
39.8
|
1.0
|
N5
|
B:NCO102
|
2.0
|
39.2
|
1.0
|
N4
|
B:NCO102
|
2.0
|
35.6
|
1.0
|
N2
|
B:NCO102
|
2.0
|
34.1
|
1.0
|
N3
|
B:NCO102
|
2.0
|
43.9
|
1.0
|
N6
|
B:NCO102
|
2.0
|
39.5
|
1.0
|
O
|
B:HOH242
|
3.6
|
35.2
|
1.0
|
O
|
B:HOH209
|
3.6
|
39.5
|
1.0
|
O6
|
B:G46
|
4.2
|
26.0
|
1.0
|
O4
|
B:U47
|
4.2
|
31.4
|
1.0
|
N7
|
B:G46
|
4.4
|
27.7
|
1.0
|
OP2
|
B:A45
|
4.7
|
42.2
|
1.0
|
C6
|
B:G46
|
5.0
|
28.9
|
1.0
|
|
Cobalt binding site 2 out
of 8 in 6uc8
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Cobalt Binding Sites List in 6uc8
Cobalt binding site 2 out
of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_02.jpg) Mono view
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Guanine Riboswitch Bound to 8-Aminoguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co103
b:21.1
occ:1.00
|
CO
|
B:NCO103
|
0.0
|
21.1
|
1.0
|
N6
|
B:NCO103
|
2.0
|
18.1
|
1.0
|
N1
|
B:NCO103
|
2.0
|
19.6
|
1.0
|
N3
|
B:NCO103
|
2.0
|
17.2
|
1.0
|
N2
|
B:NCO103
|
2.0
|
14.5
|
1.0
|
N4
|
B:NCO103
|
2.0
|
13.8
|
1.0
|
N5
|
B:NCO103
|
2.0
|
17.1
|
1.0
|
O
|
B:HOH286
|
3.8
|
14.1
|
1.0
|
OP2
|
B:A66
|
3.8
|
21.5
|
1.0
|
O6
|
B:G32
|
4.0
|
16.9
|
1.0
|
O
|
B:HOH385
|
4.0
|
21.9
|
1.0
|
O6
|
B:G31
|
4.1
|
14.0
|
1.0
|
O
|
B:HOH339
|
4.1
|
23.7
|
1.0
|
O
|
B:HOH320
|
4.2
|
14.6
|
1.0
|
O
|
B:HOH274
|
4.2
|
21.1
|
1.0
|
N7
|
B:G31
|
4.3
|
17.9
|
1.0
|
O
|
B:HOH221
|
4.4
|
23.0
|
1.0
|
O
|
B:HOH380
|
4.5
|
31.9
|
1.0
|
O
|
B:HOH217
|
4.8
|
18.3
|
1.0
|
C6
|
B:G31
|
4.8
|
17.4
|
1.0
|
C5
|
B:G31
|
4.9
|
15.9
|
1.0
|
O
|
B:HOH284
|
5.0
|
17.7
|
1.0
|
C6
|
B:G32
|
5.0
|
16.9
|
1.0
|
|
Cobalt binding site 3 out
of 8 in 6uc8
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Cobalt Binding Sites List in 6uc8
Cobalt binding site 3 out
of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_03.jpg) Mono view
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Guanine Riboswitch Bound to 8-Aminoguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co104
b:25.5
occ:1.00
|
CO
|
B:NCO104
|
0.0
|
25.5
|
1.0
|
N1
|
B:NCO104
|
2.0
|
22.3
|
1.0
|
N4
|
B:NCO104
|
2.0
|
17.0
|
1.0
|
N3
|
B:NCO104
|
2.0
|
16.9
|
1.0
|
N6
|
B:NCO104
|
2.0
|
23.6
|
1.0
|
N2
|
B:NCO104
|
2.0
|
17.6
|
1.0
|
N5
|
B:NCO104
|
2.0
|
21.7
|
1.0
|
O
|
B:HOH327
|
3.6
|
25.6
|
1.0
|
O4
|
B:U69
|
4.0
|
19.3
|
1.0
|
O
|
B:HOH334
|
4.0
|
31.1
|
1.0
|
O
|
B:HOH231
|
4.0
|
18.0
|
1.0
|
O
|
B:HOH355
|
4.0
|
20.8
|
1.0
|
O6
|
B:G56
|
4.1
|
19.4
|
1.0
|
O
|
B:HOH234
|
4.1
|
20.4
|
1.0
|
O
|
B:HOH351
|
4.3
|
20.4
|
1.0
|
OP1
|
B:C39
|
4.4
|
15.6
|
1.0
|
OP2
|
B:C39
|
4.4
|
16.8
|
1.0
|
N7
|
B:G56
|
4.4
|
20.4
|
1.0
|
O6
|
B:G68
|
4.8
|
16.1
|
1.0
|
P
|
B:C39
|
4.9
|
15.7
|
1.0
|
C6
|
B:G56
|
4.9
|
22.4
|
1.0
|
O
|
B:HOH212
|
4.9
|
30.8
|
1.0
|
|
Cobalt binding site 4 out
of 8 in 6uc8
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Cobalt Binding Sites List in 6uc8
Cobalt binding site 4 out
of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_04.jpg) Mono view
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Guanine Riboswitch Bound to 8-Aminoguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co105
b:22.6
occ:1.00
|
CO
|
B:NCO105
|
0.0
|
22.6
|
1.0
|
N4
|
B:NCO105
|
2.0
|
23.1
|
1.0
|
N3
|
B:NCO105
|
2.0
|
19.4
|
1.0
|
N6
|
B:NCO105
|
2.0
|
19.0
|
1.0
|
N5
|
B:NCO105
|
2.0
|
25.5
|
1.0
|
N1
|
B:NCO105
|
2.0
|
21.4
|
1.0
|
N2
|
B:NCO105
|
2.0
|
19.9
|
1.0
|
O
|
B:HOH314
|
3.7
|
21.5
|
1.0
|
O
|
B:HOH316
|
3.8
|
22.9
|
1.0
|
OP1
|
B:U67
|
4.0
|
17.3
|
1.0
|
O3'
|
B:A66
|
4.3
|
15.0
|
1.0
|
O
|
B:HOH386
|
4.5
|
41.5
|
1.0
|
O
|
B:HOH207
|
4.7
|
26.2
|
1.0
|
P
|
B:U67
|
4.8
|
15.2
|
1.0
|
O
|
B:HOH397
|
5.0
|
28.1
|
1.0
|
|
Cobalt binding site 5 out
of 8 in 6uc8
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Cobalt Binding Sites List in 6uc8
Cobalt binding site 5 out
of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_05.jpg) Mono view
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Guanine Riboswitch Bound to 8-Aminoguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co106
b:36.7
occ:1.00
|
CO
|
B:NCO106
|
0.0
|
36.7
|
1.0
|
N6
|
B:NCO106
|
2.0
|
32.6
|
1.0
|
N2
|
B:NCO106
|
2.0
|
27.2
|
1.0
|
N1
|
B:NCO106
|
2.0
|
28.0
|
1.0
|
N3
|
B:NCO106
|
2.0
|
27.3
|
1.0
|
N4
|
B:NCO106
|
2.0
|
23.6
|
1.0
|
N5
|
B:NCO106
|
2.0
|
20.6
|
1.0
|
O
|
B:HOH205
|
3.1
|
31.1
|
1.0
|
O
|
B:HOH262
|
3.8
|
24.3
|
1.0
|
OP2
|
B:G37
|
4.0
|
17.3
|
1.0
|
O6
|
B:G38
|
4.0
|
16.2
|
1.0
|
O
|
B:HOH348
|
4.0
|
21.9
|
1.0
|
O
|
B:HOH344
|
4.2
|
32.6
|
1.0
|
N7
|
B:G38
|
4.2
|
17.2
|
1.0
|
N7
|
B:G37
|
4.3
|
16.1
|
1.0
|
O
|
B:HOH331
|
4.6
|
26.8
|
1.0
|
C6
|
B:G38
|
4.8
|
17.1
|
1.0
|
C8
|
B:G37
|
4.9
|
17.4
|
1.0
|
C5
|
B:G38
|
4.9
|
17.4
|
1.0
|
|
Cobalt binding site 6 out
of 8 in 6uc8
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Cobalt Binding Sites List in 6uc8
Cobalt binding site 6 out
of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_06.jpg) Mono view
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Guanine Riboswitch Bound to 8-Aminoguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co107
b:27.2
occ:1.00
|
CO
|
B:NCO107
|
0.0
|
27.2
|
1.0
|
N6
|
B:NCO107
|
2.0
|
23.8
|
1.0
|
N4
|
B:NCO107
|
2.0
|
25.1
|
1.0
|
N5
|
B:NCO107
|
2.0
|
26.4
|
1.0
|
N1
|
B:NCO107
|
2.0
|
19.3
|
1.0
|
N2
|
B:NCO107
|
2.0
|
23.9
|
1.0
|
N3
|
B:NCO107
|
2.0
|
18.6
|
1.0
|
O
|
B:HOH258
|
3.7
|
24.5
|
1.0
|
O
|
B:HOH281
|
3.8
|
20.6
|
1.0
|
O
|
B:HOH356
|
3.9
|
24.0
|
1.0
|
OP1
|
B:G38
|
3.9
|
13.8
|
1.0
|
O
|
B:HOH341
|
4.0
|
21.6
|
1.0
|
O
|
B:HOH382
|
4.1
|
29.6
|
1.0
|
OP1
|
B:G56
|
4.1
|
24.4
|
1.0
|
O
|
B:HOH309
|
4.2
|
28.2
|
1.0
|
O
|
B:HOH298
|
4.3
|
31.3
|
1.0
|
O
|
B:HOH369
|
4.7
|
37.3
|
1.0
|
OP2
|
B:G56
|
4.8
|
24.3
|
1.0
|
O
|
B:HOH265
|
4.9
|
22.5
|
1.0
|
P
|
B:G56
|
4.9
|
21.9
|
1.0
|
P
|
B:G38
|
5.0
|
14.6
|
1.0
|
|
Cobalt binding site 7 out
of 8 in 6uc8
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Cobalt Binding Sites List in 6uc8
Cobalt binding site 7 out
of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_07.jpg) Mono view
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of Guanine Riboswitch Bound to 8-Aminoguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co108
b:44.0
occ:1.00
|
CO
|
B:NCO108
|
0.0
|
44.0
|
1.0
|
N1
|
B:NCO108
|
2.0
|
36.8
|
1.0
|
N2
|
B:NCO108
|
2.0
|
31.8
|
1.0
|
N5
|
B:NCO108
|
2.0
|
39.1
|
1.0
|
N3
|
B:NCO108
|
2.0
|
34.9
|
1.0
|
N6
|
B:NCO108
|
2.0
|
30.9
|
1.0
|
N4
|
B:NCO108
|
2.0
|
39.1
|
1.0
|
O
|
B:HOH269
|
3.7
|
30.3
|
1.0
|
O
|
B:HOH333
|
4.0
|
30.0
|
1.0
|
OP1
|
B:A24
|
4.1
|
27.4
|
1.0
|
O
|
B:HOH266
|
4.1
|
30.8
|
1.0
|
OP2
|
B:C71
|
4.1
|
19.7
|
1.0
|
O
|
B:HOH391
|
4.4
|
32.1
|
1.0
|
O
|
B:HOH272
|
4.6
|
39.9
|
1.0
|
O
|
B:HOH235
|
4.8
|
24.1
|
1.0
|
|
Cobalt binding site 8 out
of 8 in 6uc8
Go back to
Cobalt Binding Sites List in 6uc8
Cobalt binding site 8 out
of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_08.jpg) Mono view
![](/pictures/CO/pdb/uc/6uc8-CO-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 8 of Guanine Riboswitch Bound to 8-Aminoguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co109
b:55.2
occ:1.00
|
CO
|
B:NCO109
|
0.0
|
55.2
|
1.0
|
N3
|
B:NCO109
|
2.0
|
29.7
|
1.0
|
N2
|
B:NCO109
|
2.0
|
37.4
|
1.0
|
N4
|
B:NCO109
|
2.0
|
42.7
|
1.0
|
N1
|
B:NCO109
|
2.0
|
36.2
|
1.0
|
N6
|
B:NCO109
|
2.0
|
27.9
|
1.0
|
N5
|
B:NCO109
|
2.0
|
45.9
|
1.0
|
O
|
B:HOH300
|
3.8
|
27.7
|
1.0
|
OP1
|
B:G72
|
4.1
|
12.9
|
1.0
|
OP2
|
B:A73
|
4.7
|
21.9
|
1.0
|
O
|
B:HOH305
|
5.0
|
33.4
|
1.0
|
|
Reference:
M.M.Matyjasik,
S.D.Hall,
R.T.Batey.
High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 32414072
DOI: 10.3390/MOLECULES25102295
Page generated: Tue Jul 30 18:59:55 2024
|