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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 site 1 out of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine


Mono view


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 site 2 out of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine


Mono view


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 site 3 out of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine


Mono view


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 site 4 out of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine


Mono view


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 site 5 out of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine


Mono view


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 site 6 out of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine


Mono view


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 site 7 out of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine


Mono view


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

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Cobalt binding site 8 out of 8 in the Guanine Riboswitch Bound to 8-Aminoguanine


Mono view


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

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