Atomistry » Cobalt » PDB 6oxd-6vv9 » 6uc8
Atomistry »
  Cobalt »
    PDB 6oxd-6vv9 »
      6uc8 »

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

Go back to Cobalt Binding Sites List in 6uc8
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

Go back to Cobalt Binding Sites List in 6uc8
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

Go back to Cobalt Binding Sites List in 6uc8
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

Go back to Cobalt Binding Sites List in 6uc8
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

Go back to Cobalt Binding Sites List in 6uc8
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

Go back to Cobalt Binding Sites List in 6uc8
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

Go back to Cobalt Binding Sites List in 6uc8
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

Go back to Cobalt Binding Sites List in 6uc8
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy