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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

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Cobalt binding site 1 out of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine


Mono view


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 site 2 out of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine


Mono view


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 site 3 out of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine


Mono view


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 site 4 out of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine


Mono view


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

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Cobalt binding site 5 out of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine


Mono view


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 site 6 out of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine


Mono view


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

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Cobalt binding site 7 out of 7 in the 1.60 A Resolution Structure of the Guanine Riboswitch Bound to Guanine


Mono view


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

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