Atomistry » Cobalt » PDB 6oxc-6vv8 » 6ubu
Atomistry »
  Cobalt »
    PDB 6oxc-6vv8 »
      6ubu »

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


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

Go back to 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


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

Go back to 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


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

Go back to 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


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

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


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

Go back to 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


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

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


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: Sun Dec 13 10:51:42 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy