Cobalt in PDB 6ubu: 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
Protein crystallography data
The structure of 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine, PDB code: 6ubu
was solved by
M.M.Matyjasik,
R.T.Batey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.66 /
1.60
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
132.175,
35.260,
42.276,
90.00,
90.86,
90.00
|
R / Rfree (%)
|
20 /
22
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
(pdb code 6ubu). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the
1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine, PDB code: 6ubu:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
Cobalt binding site 1 out
of 7 in 6ubu
Go back to
Cobalt Binding Sites List in 6ubu
Cobalt binding site 1 out
of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
![](/pictures/CO/pdb/ub/6ubu-CO-sphere_01.jpg) Mono view
![](/pictures/CO/pdb/ub/6ubu-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 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co101
b:37.0
occ:1.00
|
CO
|
B:NCO101
|
0.0
|
37.0
|
1.0
|
N6
|
B:NCO101
|
2.0
|
33.5
|
1.0
|
N4
|
B:NCO101
|
2.0
|
38.2
|
1.0
|
N2
|
B:NCO101
|
2.0
|
31.3
|
1.0
|
N3
|
B:NCO101
|
2.0
|
32.5
|
1.0
|
N1
|
B:NCO101
|
2.0
|
37.9
|
1.0
|
N5
|
B:NCO101
|
2.0
|
34.1
|
1.0
|
OP2
|
B:C71
|
4.1
|
20.4
|
1.0
|
OP1
|
B:A24
|
4.1
|
27.5
|
1.0
|
O
|
B:HOH345
|
4.2
|
30.1
|
1.0
|
O
|
B:HOH359
|
4.2
|
34.0
|
1.0
|
O
|
B:HOH400
|
4.3
|
37.2
|
1.0
|
O
|
B:HOH259
|
4.5
|
22.6
|
1.0
|
O
|
B:HOH211
|
4.6
|
33.7
|
1.0
|
|
Cobalt binding site 2 out
of 7 in 6ubu
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Cobalt Binding Sites List in 6ubu
Cobalt binding site 2 out
of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
![](/pictures/CO/pdb/ub/6ubu-CO-sphere_02.jpg) Mono view
![](/pictures/CO/pdb/ub/6ubu-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 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co102
b:22.1
occ:1.00
|
CO
|
B:NCO102
|
0.0
|
22.1
|
1.0
|
N6
|
B:NCO102
|
2.0
|
19.8
|
1.0
|
N1
|
B:NCO102
|
2.0
|
20.5
|
1.0
|
N5
|
B:NCO102
|
2.0
|
19.4
|
1.0
|
N3
|
B:NCO102
|
2.0
|
19.7
|
1.0
|
N4
|
B:NCO102
|
2.0
|
20.3
|
1.0
|
N2
|
B:NCO102
|
2.0
|
17.8
|
1.0
|
OP2
|
B:A66
|
3.9
|
22.4
|
1.0
|
O
|
B:HOH274
|
4.0
|
19.6
|
1.0
|
O6
|
B:G32
|
4.0
|
18.9
|
1.0
|
O6
|
B:G31
|
4.1
|
17.6
|
1.0
|
O
|
B:HOH357
|
4.2
|
22.1
|
1.0
|
O
|
B:HOH339
|
4.2
|
20.1
|
1.0
|
O
|
B:HOH318
|
4.3
|
21.5
|
1.0
|
N7
|
B:G31
|
4.3
|
17.6
|
1.0
|
O
|
B:HOH234
|
4.4
|
24.2
|
1.0
|
O
|
B:HOH281
|
4.4
|
20.4
|
1.0
|
C6
|
B:G31
|
4.8
|
17.9
|
1.0
|
O
|
B:HOH275
|
4.9
|
22.2
|
1.0
|
C5
|
B:G31
|
4.9
|
17.6
|
1.0
|
O
|
B:HOH256
|
5.0
|
19.9
|
1.0
|
C6
|
B:G32
|
5.0
|
19.6
|
1.0
|
|
Cobalt binding site 3 out
of 7 in 6ubu
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Cobalt Binding Sites List in 6ubu
Cobalt binding site 3 out
of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
![](/pictures/CO/pdb/ub/6ubu-CO-sphere_03.jpg) Mono view
![](/pictures/CO/pdb/ub/6ubu-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 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co103
b:22.5
occ:1.00
|
CO
|
B:NCO103
|
0.0
|
22.5
|
1.0
|
N6
|
B:NCO103
|
2.0
|
23.0
|
1.0
|
N4
|
B:NCO103
|
2.0
|
27.2
|
1.0
|
N2
|
B:NCO103
|
2.0
|
20.5
|
1.0
|
N5
|
B:NCO103
|
2.0
|
23.8
|
1.0
|
N3
|
B:NCO103
|
2.0
|
19.4
|
1.0
|
N1
|
B:NCO103
|
2.0
|
20.1
|
1.0
|
O
|
B:HOH356
|
3.9
|
25.7
|
1.0
|
OP1
|
B:U67
|
4.1
|
16.0
|
1.0
|
O
|
B:HOH229
|
4.1
|
31.3
|
1.0
|
O
|
B:HOH384
|
4.2
|
29.8
|
1.0
|
O
|
B:HOH383
|
4.2
|
44.7
|
1.0
|
O3'
|
B:A66
|
4.3
|
17.8
|
1.0
|
O
|
B:HOH403
|
4.5
|
30.9
|
1.0
|
P
|
B:U67
|
4.9
|
16.5
|
1.0
|
|
Cobalt binding site 4 out
of 7 in 6ubu
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Cobalt Binding Sites List in 6ubu
Cobalt binding site 4 out
of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
![](/pictures/CO/pdb/ub/6ubu-CO-sphere_04.jpg) Mono view
![](/pictures/CO/pdb/ub/6ubu-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 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co104
b:22.8
occ:1.00
|
CO
|
B:NCO104
|
0.0
|
22.8
|
1.0
|
N4
|
B:NCO104
|
2.0
|
20.1
|
1.0
|
N3
|
B:NCO104
|
2.0
|
20.5
|
1.0
|
N5
|
B:NCO104
|
2.0
|
20.1
|
1.0
|
N1
|
B:NCO104
|
2.0
|
20.5
|
1.0
|
N6
|
B:NCO104
|
2.0
|
24.2
|
1.0
|
N2
|
B:NCO104
|
2.0
|
21.3
|
1.0
|
O
|
B:HOH262
|
3.9
|
27.7
|
1.0
|
O4
|
B:U69
|
3.9
|
18.8
|
1.0
|
O
|
B:HOH349
|
4.0
|
27.6
|
1.0
|
O
|
B:HOH222
|
4.1
|
27.8
|
1.0
|
O6
|
B:G56
|
4.1
|
18.7
|
1.0
|
O
|
B:HOH346
|
4.2
|
25.1
|
1.0
|
O
|
B:HOH231
|
4.2
|
21.6
|
1.0
|
O
|
B:HOH385
|
4.2
|
31.2
|
1.0
|
O
|
B:HOH319
|
4.2
|
24.6
|
1.0
|
OP2
|
B:C39
|
4.3
|
21.0
|
1.0
|
OP1
|
B:C39
|
4.4
|
23.5
|
1.0
|
N7
|
B:G56
|
4.6
|
18.6
|
1.0
|
O6
|
B:G68
|
4.8
|
18.4
|
1.0
|
P
|
B:C39
|
4.9
|
20.5
|
1.0
|
O
|
B:HOH287
|
4.9
|
29.5
|
1.0
|
O
|
B:HOH221
|
5.0
|
27.2
|
1.0
|
|
Cobalt binding site 5 out
of 7 in 6ubu
Go back to
Cobalt Binding Sites List in 6ubu
Cobalt binding site 5 out
of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
![](/pictures/CO/pdb/ub/6ubu-CO-sphere_05.jpg) Mono view
![](/pictures/CO/pdb/ub/6ubu-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 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co105
b:32.8
occ:1.00
|
CO
|
B:NCO105
|
0.0
|
32.8
|
1.0
|
N6
|
B:NCO105
|
2.0
|
28.4
|
1.0
|
N3
|
B:NCO105
|
2.0
|
31.4
|
1.0
|
N4
|
B:NCO105
|
2.0
|
25.1
|
1.0
|
N2
|
B:NCO105
|
2.0
|
29.5
|
1.0
|
N5
|
B:NCO105
|
2.0
|
24.2
|
1.0
|
N1
|
B:NCO105
|
2.0
|
24.7
|
1.0
|
O
|
B:HOH367
|
4.0
|
24.9
|
1.0
|
O6
|
B:G38
|
4.0
|
18.0
|
1.0
|
OP2
|
B:G37
|
4.1
|
19.0
|
1.0
|
N7
|
B:G38
|
4.3
|
19.8
|
1.0
|
N7
|
B:G37
|
4.3
|
18.4
|
1.0
|
O
|
B:HOH317
|
4.3
|
27.8
|
1.0
|
O
|
B:HOH347
|
4.8
|
28.2
|
1.0
|
O
|
B:HOH337
|
4.8
|
34.7
|
1.0
|
C6
|
B:G38
|
4.8
|
18.6
|
1.0
|
C8
|
B:G37
|
4.9
|
18.6
|
1.0
|
O
|
B:HOH279
|
4.9
|
22.2
|
1.0
|
C5
|
B:G38
|
4.9
|
20.3
|
1.0
|
|
Cobalt binding site 6 out
of 7 in 6ubu
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Cobalt Binding Sites List in 6ubu
Cobalt binding site 6 out
of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
![](/pictures/CO/pdb/ub/6ubu-CO-sphere_06.jpg) Mono view
![](/pictures/CO/pdb/ub/6ubu-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 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co106
b:28.4
occ:1.00
|
CO
|
B:NCO106
|
0.0
|
28.4
|
1.0
|
N5
|
B:NCO106
|
2.0
|
28.5
|
1.0
|
N4
|
B:NCO106
|
2.0
|
26.4
|
1.0
|
N6
|
B:NCO106
|
2.0
|
25.0
|
1.0
|
N2
|
B:NCO106
|
2.0
|
33.9
|
1.0
|
N3
|
B:NCO106
|
2.0
|
24.7
|
1.0
|
N1
|
B:NCO106
|
2.0
|
23.6
|
1.0
|
O
|
B:HOH276
|
3.7
|
27.0
|
1.0
|
O
|
B:HOH220
|
3.9
|
27.8
|
1.0
|
OP1
|
B:G38
|
3.9
|
18.7
|
1.0
|
O
|
B:HOH242
|
4.1
|
24.7
|
1.0
|
O
|
B:HOH397
|
4.1
|
31.6
|
1.0
|
O
|
B:HOH247
|
4.1
|
30.2
|
1.0
|
OP1
|
B:G56
|
4.3
|
25.1
|
1.0
|
OP2
|
B:G56
|
4.7
|
21.5
|
1.0
|
P
|
B:G38
|
5.0
|
17.1
|
1.0
|
|
Cobalt binding site 7 out
of 7 in 6ubu
Go back to
Cobalt Binding Sites List in 6ubu
Cobalt binding site 7 out
of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine
![](/pictures/CO/pdb/ub/6ubu-CO-sphere_07.jpg) Mono view
![](/pictures/CO/pdb/ub/6ubu-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 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co107
b:54.3
occ:1.00
|
CO
|
B:NCO107
|
0.0
|
54.3
|
1.0
|
N3
|
B:NCO107
|
2.0
|
41.8
|
1.0
|
N5
|
B:NCO107
|
2.0
|
40.2
|
1.0
|
N1
|
B:NCO107
|
2.0
|
44.8
|
1.0
|
N4
|
B:NCO107
|
2.0
|
47.5
|
1.0
|
N2
|
B:NCO107
|
2.0
|
34.4
|
1.0
|
N6
|
B:NCO107
|
2.0
|
27.8
|
1.0
|
OP1
|
B:G72
|
4.0
|
17.8
|
1.0
|
O
|
B:HOH394
|
4.3
|
45.8
|
1.0
|
OP2
|
B:A73
|
4.5
|
24.6
|
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 18:59:37 2024
|