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Cobalt in PDB 4feo: Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine

Protein crystallography data

The structure of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine, PDB code: 4feo was solved by C.D.Stoddard, J.J.Trausch, J.Widmann, J.Marcano, R.Knight, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.910, 35.230, 41.460, 90.00, 90.36, 90.00
R / Rfree (%) 17.4 / 22.8

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine (pdb code 4feo). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine, PDB code: 4feo:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cobalt binding site 1 out of 9 in 4feo

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Cobalt binding site 1 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:14.6
occ:1.00
 CO B:NCO102 0.0 14.6 1.0
N1 B:NCO102 2.0 15.6 1.0
N2 B:NCO102 2.0 15.3 1.0
N5 B:NCO102 2.0 12.8 1.0
N6 B:NCO102 2.0 14.7 1.0
N4 B:NCO102 2.0 15.0 1.0
N3 B:NCO102 2.0 15.1 1.0
O B:HOH566 3.7 22.2 1.0
O B:HOH311 3.8 15.7 1.0
O B:HOH361 3.9 16.7 1.0
O B:HOH422 3.9 22.9 1.0
O B:HOH509 4.0 18.1 1.0
OP1 B:U67 4.1 11.1 1.0
O B:HOH493 4.3 31.1 1.0
O3' B:A66 4.3 11.0 1.0
O B:HOH456 4.4 16.6 1.0
P B:U67 4.9 10.0 1.0
O2' B:A66 4.9 11.7 1.0

Cobalt binding site 2 out of 9 in 4feo

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Cobalt binding site 2 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co103

b:29.0
occ:1.00
 CO B:NCO103 0.0 29.0 1.0
N3 B:NCO103 2.0 25.4 1.0
N2 B:NCO103 2.0 25.9 1.0
N4 B:NCO103 2.0 26.2 1.0
N6 B:NCO103 2.0 25.1 1.0
N5 B:NCO103 2.0 26.5 1.0
N1 B:NCO103 2.0 26.2 1.0
O B:HOH331 3.8 18.2 1.0
OP1 B:G38 3.8 10.7 1.0
O B:HOH697 3.8 26.8 1.0
O B:HOH746 3.9 37.1 1.0
O B:HOH271 4.1 23.9 1.0
OP1 B:G56 4.1 20.9 1.0
O B:HOH575 4.1 25.6 1.0
O B:HOH712 4.7 42.4 1.0
O B:HOH313 4.8 45.5 1.0
P B:G38 4.9 9.6 1.0
OP2 B:G56 4.9 19.1 1.0
O B:HOH465 4.9 32.3 1.0
OP2 B:G38 5.0 12.1 1.0
O B:HOH268 5.0 23.6 1.0

Cobalt binding site 3 out of 9 in 4feo

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Cobalt binding site 3 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co104

b:19.1
occ:1.00
 CO B:NCO104 0.0 19.1 1.0
N6 B:NCO104 1.9 20.2 1.0
N3 B:NCO104 2.0 16.0 1.0
N1 B:NCO104 2.0 19.2 1.0
N4 B:NCO104 2.0 21.9 1.0
N2 B:NCO104 2.0 20.3 1.0
N5 B:NCO104 2.0 19.8 1.0
O B:HOH450 3.9 20.6 1.0
O B:HOH306 4.0 22.2 1.0
O4 B:U69 4.0 10.3 1.0
O B:HOH347 4.0 24.4 1.0
O6 B:G56 4.1 15.3 1.0
O B:HOH250 4.1 22.0 1.0
O B:HOH714 4.1 54.8 1.0
O B:HOH620 4.2 39.8 1.0
O B:HOH224 4.2 17.0 1.0
O B:HOH728 4.4 56.5 1.0
O B:HOH706 4.4 31.0 1.0
OP2 B:C39 4.4 13.7 1.0
N7 B:G56 4.5 14.5 1.0
OP1 B:C39 4.5 11.9 1.0
O B:HOH651 4.5 0.7 1.0
O6 B:G68 4.8 12.5 1.0
C6 B:G56 4.9 15.0 1.0
O B:HOH511 5.0 28.7 1.0

Cobalt binding site 4 out of 9 in 4feo

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Cobalt binding site 4 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co105

b:12.6
occ:1.00
 CO B:NCO105 0.0 12.6 1.0
N1 B:NCO105 2.0 10.2 1.0
N2 B:NCO105 2.0 11.1 1.0
N6 B:NCO105 2.0 10.8 1.0
N5 B:NCO105 2.0 12.3 1.0
N3 B:NCO105 2.0 11.2 1.0
N4 B:NCO105 2.0 8.8 1.0
OP2 B:A66 3.8 14.1 1.0
O B:HOH214 3.8 13.6 1.0
O6 B:G32 3.9 11.6 1.0
O B:HOH276 4.0 14.8 1.0
O6 B:G31 4.0 13.6 1.0
O B:HOH231 4.1 13.6 1.0
O B:HOH442 4.2 19.1 1.0
O B:HOH305 4.2 12.9 1.0
O B:HOH212 4.2 10.3 1.0
O B:HOH254 4.2 13.6 1.0
O B:HOH227 4.2 13.7 1.0
N7 B:G31 4.3 10.6 1.0
C6 B:G31 4.8 11.0 1.0
O B:HOH206 4.9 12.5 1.0
O4 B:U30 4.9 11.9 1.0
C6 B:G32 4.9 11.8 1.0
C5 B:G31 5.0 10.1 1.0

Cobalt binding site 5 out of 9 in 4feo

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Cobalt binding site 5 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co106

b:33.3
occ:1.00
 CO B:NCO106 0.0 33.3 1.0
N5 B:NCO106 2.0 34.1 1.0
N4 B:NCO106 2.0 34.9 1.0
N1 B:NCO106 2.0 33.6 1.0
N6 B:NCO106 2.0 33.2 1.0
N2 B:NCO106 2.0 33.4 1.0
N3 B:NCO106 2.0 31.5 1.0
O B:HOH461 3.7 23.2 1.0
O B:HOH316 3.8 27.5 1.0
OP2 B:G37 4.0 13.8 1.0
O B:HOH258 4.0 18.6 1.0
O B:HOH364 4.1 24.2 1.0
O6 B:G38 4.1 12.1 1.0
N7 B:G38 4.2 10.8 1.0
O B:HOH851 4.3 41.6 1.0
O B:HOH379 4.4 25.1 1.0
N7 B:G37 4.5 12.2 1.0
O B:HOH569 4.6 22.9 1.0
O B:HOH407 4.7 25.3 1.0
C6 B:G38 4.9 10.8 1.0
O B:HOH339 4.9 23.9 1.0
C5 B:G38 5.0 10.6 1.0
O B:HOH431 5.0 39.9 1.0

Cobalt binding site 6 out of 9 in 4feo

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Cobalt binding site 6 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co107

b:81.3
occ:1.00
 CO B:NCO107 0.0 81.3 1.0
N4 B:NCO107 2.0 81.0 1.0
N6 B:NCO107 2.0 81.1 1.0
N5 B:NCO107 2.0 81.2 1.0
N1 B:NCO107 2.0 81.1 1.0
N2 B:NCO107 2.0 80.9 1.0
N3 B:NCO107 2.0 81.0 1.0
O B:HOH341 3.2 26.6 1.0
O B:HOH409 3.5 23.0 1.0
O B:HOH721 3.8 0.8 1.0
O B:HOH615 3.8 55.4 1.0
O B:HOH577 3.9 33.4 1.0
OP1 B:C54 4.0 24.4 1.0
OP2 B:C41 4.2 14.1 1.0
O B:HOH640 4.3 41.4 1.0
OP1 B:C53 4.3 20.2 1.0
O B:HOH613 4.3 43.9 1.0
O5' B:C54 4.4 19.2 1.0
O B:HOH590 4.6 35.5 1.0
OP2 B:C53 4.8 21.3 1.0
O B:HOH348 4.8 33.4 1.0
O B:HOH516 4.8 34.7 1.0
P B:C54 4.9 21.8 1.0
P B:C53 4.9 21.0 1.0
O B:HOH228 5.0 15.5 1.0

Cobalt binding site 7 out of 9 in 4feo

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Cobalt binding site 7 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co108

b:24.9
occ:1.00
 CO B:NCO108 0.0 24.9 1.0
N4 B:NCO108 2.0 24.6 1.0
N5 B:NCO108 2.0 24.6 1.0
N6 B:NCO108 2.0 24.5 1.0
N2 B:NCO108 2.0 24.7 1.0
N1 B:NCO108 2.0 23.8 1.0
N3 B:NCO108 2.0 25.1 1.0
O B:HOH675 3.9 51.8 1.0
O B:HOH392 3.9 30.1 1.0
O B:HOH528 3.9 36.3 1.0
O B:HOH366 4.0 36.6 1.0
O B:HOH520 4.0 55.5 1.0
O B:HOH595 4.1 33.1 1.0
O B:HOH226 4.1 22.7 1.0
O6 B:G46 4.1 15.1 1.0
O4 B:U47 4.2 21.3 1.0
O B:HOH328 4.3 24.5 1.0
N7 B:G46 4.3 18.2 1.0
O B:HOH290 4.5 30.1 1.0
O B:HOH255 4.9 33.8 1.0
C6 B:G46 4.9 17.8 1.0
O B:HOH462 5.0 27.0 1.0

Cobalt binding site 8 out of 9 in 4feo

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Cobalt binding site 8 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co109

b:0.7
occ:1.00
 CO B:NCO109 0.0 0.7 1.0
N4 B:NCO109 2.0 0.5 1.0
N6 B:NCO109 2.0 0.5 1.0
N5 B:NCO109 2.0 0.5 1.0
N2 B:NCO109 2.0 0.5 1.0
N1 B:NCO109 2.0 0.6 1.0
N3 B:NCO109 2.0 0.5 1.0
O B:HOH416 3.7 31.7 1.0
O B:HOH859 3.9 64.8 1.0
OP1 B:A21 4.0 21.9 1.0
O B:HOH624 4.1 53.5 1.0
O B:HOH855 4.1 65.5 1.0
OP2 B:U22 4.4 18.0 1.0
O B:HOH676 4.4 53.8 1.0
O B:HOH669 4.5 42.1 1.0
O B:HOH685 4.7 47.8 1.0
O B:HOH663 4.7 51.0 1.0
O B:HOH593 5.0 32.8 1.0

Cobalt binding site 9 out of 9 in 4feo

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Cobalt binding site 9 out of 9 in the Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of the AU25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co110

b:29.9
occ:0.64
 CO B:NCO110 0.0 29.9 0.6
N4 B:NCO110 2.0 28.1 0.6
N2 B:NCO110 2.0 29.8 0.6
N5 B:NCO110 2.0 30.1 0.6
N6 B:NCO110 2.0 29.1 0.6
N1 B:NCO110 2.0 30.4 0.6
N3 B:NCO110 2.0 29.4 0.6
O B:HOH443 3.8 56.0 1.0
OP1 B:G72 4.2 13.3 1.0
O B:HOH703 4.3 49.2 1.0
O B:HOH787 4.6 52.3 1.0
OP2 B:A73 5.0 23.6 1.0
O B:HOH589 5.0 30.6 1.0

Reference:

C.D.Stoddard, J.Widmann, J.J.Trausch, J.G.Marcano-Velazquez, R.Knight, R.T.Batey. Nucleotides Adjacent to the Ligand-Binding Pocket Are Linked to Activity Tuning in the Purine Riboswitch. J.Mol.Biol. V. 425 1596 2013.
ISSN: ISSN 0022-2836
PubMed: 23485418
DOI: 10.1016/J.JMB.2013.02.023
Page generated: Tue Jul 30 17:04:35 2024

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