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Cobalt in PDB 6uc9: Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine

Protein crystallography data

The structure of Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine, PDB code: 6uc9 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) 19.86 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.468, 35.171, 41.889, 90.00, 91.55, 90.00
R / Rfree (%) 18.7 / 21.1

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine (pdb code 6uc9). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine, PDB code: 6uc9:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in 6uc9

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Cobalt binding site 1 out of 7 in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine


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 O6-Cyclohexylmethyl Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co101

b:29.9
occ:1.00
 CO B:NCO101 0.0 29.9 1.0
N1 B:NCO101 2.0 31.6 1.0
N5 B:NCO101 2.0 28.4 1.0
N4 B:NCO101 2.0 24.0 1.0
N2 B:NCO101 2.0 28.1 1.0
N6 B:NCO101 2.0 35.3 1.0
N3 B:NCO101 2.0 23.6 1.0
O B:HOH242 3.8 27.2 1.0
O B:HOH215 3.8 27.2 1.0
O4 B:U69 3.9 20.7 1.0
O6 B:G56 4.0 21.6 1.0
O B:HOH361 4.1 36.1 1.0
O B:HOH217 4.2 25.6 1.0
O B:HOH334 4.4 24.7 1.0
N7 B:G56 4.5 24.3 1.0
OP1 B:C39 4.5 19.9 1.0
OP2 B:C39 4.6 21.4 1.0
O B:HOH238 4.6 42.7 1.0
O6 B:G68 4.7 17.7 1.0
C6 B:G56 4.8 25.1 1.0
O B:HOH212 4.9 30.7 1.0

Cobalt binding site 2 out of 7 in 6uc9

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Cobalt binding site 2 out of 7 in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine


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 O6-Cyclohexylmethyl Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:25.0
occ:1.00
 CO B:NCO102 0.0 25.0 1.0
N6 B:NCO102 2.0 21.2 1.0
N4 B:NCO102 2.0 25.5 1.0
N5 B:NCO102 2.0 25.1 1.0
N2 B:NCO102 2.0 19.0 1.0
N3 B:NCO102 2.0 19.8 1.0
N1 B:NCO102 2.0 18.9 1.0
O B:HOH317 3.6 40.0 1.0
O B:HOH279 3.9 20.4 1.0
O B:HOH336 3.9 23.7 1.0
O B:HOH214 4.0 27.3 1.0
O B:HOH350 4.0 33.4 1.0
OP1 B:U67 4.1 17.3 1.0
O B:HOH342 4.2 30.8 1.0
O3' B:A66 4.3 17.1 1.0
P B:U67 4.9 17.7 1.0

Cobalt binding site 3 out of 7 in 6uc9

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Cobalt binding site 3 out of 7 in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine


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 O6-Cyclohexylmethyl Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co103

b:30.9
occ:1.00
 CO B:NCO103 0.0 30.9 1.0
N5 B:NCO103 2.0 27.5 1.0
N4 B:NCO103 2.0 23.3 1.0
N6 B:NCO103 2.0 23.3 1.0
N1 B:NCO103 2.0 24.4 1.0
N3 B:NCO103 2.0 23.8 1.0
N2 B:NCO103 2.0 24.6 1.0
O B:HOH220 3.7 26.0 1.0
O B:HOH276 3.8 30.4 1.0
OP1 B:G56 3.9 34.2 1.0
O B:HOH311 3.9 24.0 1.0
OP1 B:G38 3.9 18.6 1.0
O B:HOH315 4.0 25.2 1.0
O B:HOH363 4.0 24.7 1.0
O B:HOH378 4.9 29.7 1.0
P B:G56 4.9 28.1 1.0

Cobalt binding site 4 out of 7 in 6uc9

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Cobalt binding site 4 out of 7 in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine


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 O6-Cyclohexylmethyl Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co104

b:21.5
occ:1.00
 CO B:NCO104 0.0 21.5 1.0
N4 B:NCO104 2.0 17.6 1.0
N6 B:NCO104 2.0 16.9 1.0
N1 B:NCO104 2.0 20.1 1.0
N3 B:NCO104 2.0 17.2 1.0
N5 B:NCO104 2.0 15.8 1.0
N2 B:NCO104 2.0 14.8 1.0
OP2 B:A66 3.8 22.5 1.0
O6 B:G32 3.9 20.2 1.0
O B:HOH255 4.0 19.2 1.0
O B:HOH299 4.1 16.7 1.0
O6 B:G31 4.1 17.8 1.0
O B:HOH297 4.1 19.4 1.0
O B:HOH347 4.1 23.5 1.0
O B:HOH250 4.2 18.5 1.0
O B:HOH374 4.2 23.6 1.0
O B:HOH271 4.3 17.4 1.0
N7 B:G31 4.3 16.8 1.0
O B:HOH369 4.5 30.4 1.0
O B:HOH266 4.9 21.4 1.0
C6 B:G31 4.9 19.1 1.0
C5 B:G31 4.9 20.0 1.0
C6 B:G32 4.9 19.1 1.0
O2' B:A65 5.0 20.8 1.0

Cobalt binding site 5 out of 7 in 6uc9

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Cobalt binding site 5 out of 7 in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine


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 O6-Cyclohexylmethyl Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co105

b:59.0
occ:1.00
 CO B:NCO105 0.0 59.0 1.0
N3 B:NCO105 2.0 40.9 1.0
N2 B:NCO105 2.0 30.5 1.0
N6 B:NCO105 2.0 35.9 1.0
N4 B:NCO105 2.0 42.6 1.0
N1 B:NCO105 2.0 34.9 1.0
N5 B:NCO105 2.0 34.6 1.0
O B:HOH222 3.8 36.1 1.0
OP1 B:C54 3.9 27.8 1.0
OP2 B:C41 4.0 26.0 1.0
O B:HOH322 4.1 34.9 1.0
O B:HOH352 4.3 38.5 1.0
O B:HOH262 4.4 25.2 1.0
O B:HOH234 4.4 21.8 1.0
O B:HOH207 4.4 28.6 1.0
OP2 B:G42 4.7 22.9 1.0
O5' B:C54 4.7 27.4 1.0
OP1 B:C53 4.9 35.7 1.0
P B:C41 5.0 20.2 1.0
P B:C54 5.0 26.7 1.0

Cobalt binding site 6 out of 7 in 6uc9

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Cobalt binding site 6 out of 7 in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine


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 O6-Cyclohexylmethyl Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co106

b:51.8
occ:1.00
 CO B:NCO106 0.0 51.8 1.0
N2 B:NCO106 2.0 34.5 1.0
N5 B:NCO106 2.0 45.0 1.0
N4 B:NCO106 2.0 31.1 1.0
N6 B:NCO106 2.0 41.0 1.0
N1 B:NCO106 2.0 39.0 1.0
N3 B:NCO106 2.0 36.0 1.0
O B:HOH233 4.0 36.1 1.0
O4 B:U47 4.1 30.0 1.0
O6 B:G46 4.1 24.4 1.0
N7 B:G46 4.5 28.7 1.0
O B:HOH335 4.8 44.4 1.0
C6 B:G46 5.0 28.0 1.0
C4 B:U47 5.0 28.5 1.0

Cobalt binding site 7 out of 7 in 6uc9

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Cobalt binding site 7 out of 7 in the Guanine Riboswitch Bound to O6-Cyclohexylmethyl Guanine


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 O6-Cyclohexylmethyl Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co107

b:70.8
occ:1.00
 CO B:NCO107 0.0 70.8 1.0
N4 B:NCO107 2.0 49.7 1.0
N3 B:NCO107 2.0 44.4 1.0
N6 B:NCO107 2.0 44.3 1.0
N1 B:NCO107 2.0 49.1 1.0
N5 B:NCO107 2.0 41.4 1.0
N2 B:NCO107 2.0 39.4 1.0
O B:HOH288 3.8 31.4 1.0
OP1 B:A24 4.0 25.5 1.0
OP2 B:C71 4.0 25.1 1.0
O B:HOH304 5.0 25.2 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 18:59:59 2024

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