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Cobalt in PDB 2eew: Guanine Riboswitch U47C Mutant Bound to Hypoxanthine

Protein crystallography data

The structure of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine, PDB code: 2eew was solved by S.D.Gilbert, C.E.Love, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.85 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.107, 35.258, 42.010, 90.00, 90.83, 90.00
R / Rfree (%) 23.4 / 28.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine (pdb code 2eew). 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 U47C Mutant Bound to Hypoxanthine, PDB code: 2eew:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 2eew

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Cobalt binding site 1 out of 8 in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co101

b:23.2
occ:1.00
 CO A:NCO101 0.0 23.2 1.0
N4 A:NCO101 2.0 23.4 1.0
N3 A:NCO101 2.0 23.0 1.0
N1 A:NCO101 2.0 17.9 1.0
N2 A:NCO101 2.0 22.6 1.0
N6 A:NCO101 2.0 21.6 1.0
N5 A:NCO101 2.0 23.5 1.0
O A:HOH167 3.9 29.0 1.0
OP1 A:U67 3.9 16.3 1.0
O A:HOH286 3.9 62.1 1.0
O A:HOH154 4.1 26.6 1.0
O A:HOH175 4.1 36.0 1.0
O A:HOH322 4.2 38.7 1.0
O A:HOH336 4.2 28.9 1.0
O3' A:A66 4.4 17.5 1.0
O A:HOH212 4.6 29.9 1.0
P A:U67 4.8 20.4 1.0
O A:HOH342 4.9 42.0 1.0

Cobalt binding site 2 out of 8 in 2eew

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Cobalt binding site 2 out of 8 in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:33.2
occ:1.00
 CO A:NCO102 0.0 33.2 1.0
N2 A:NCO102 2.0 32.8 1.0
N3 A:NCO102 2.0 30.6 1.0
N4 A:NCO102 2.0 31.2 1.0
N1 A:NCO102 2.0 30.4 1.0
N5 A:NCO102 2.0 32.9 1.0
N6 A:NCO102 2.0 30.2 1.0
O A:HOH119 3.7 22.3 1.0
OP1 A:G38 3.8 17.5 1.0
O A:HOH206 4.0 25.2 1.0
OP1 A:G56 4.1 31.4 1.0
O A:HOH160 4.1 25.9 1.0
O A:HOH262 4.2 30.5 1.0
O A:HOH332 4.5 42.9 1.0
O A:HOH279 4.8 31.5 1.0
OP2 A:G56 4.9 31.0 1.0
P A:G38 5.0 17.4 1.0

Cobalt binding site 3 out of 8 in 2eew

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Cobalt binding site 3 out of 8 in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:30.4
occ:1.00
 CO A:NCO103 0.0 30.4 1.0
N4 A:NCO103 2.0 30.6 1.0
N3 A:NCO103 2.0 28.7 1.0
N6 A:NCO103 2.0 29.3 1.0
N2 A:NCO103 2.0 31.5 1.0
N1 A:NCO103 2.0 28.6 1.0
N5 A:NCO103 2.0 30.9 1.0
O A:HOH248 3.7 42.0 1.0
O4 A:U69 4.0 23.2 1.0
O A:HOH176 4.1 25.6 1.0
O A:HOH177 4.1 38.5 1.0
O6 A:G56 4.1 29.2 1.0
OP2 A:C39 4.1 29.4 1.0
O A:HOH253 4.3 40.0 1.0
O A:HOH153 4.4 33.8 1.0
N7 A:G56 4.5 27.3 1.0
O A:HOH115 4.5 25.1 1.0
O6 A:G68 4.7 16.9 1.0
C6 A:G56 4.9 27.8 1.0

Cobalt binding site 4 out of 8 in 2eew

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Cobalt binding site 4 out of 8 in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co104

b:32.0
occ:1.00
 CO A:NCO104 0.0 32.0 1.0
N5 A:NCO104 2.0 31.2 1.0
N6 A:NCO104 2.0 31.0 1.0
N1 A:NCO104 2.0 31.4 1.0
N2 A:NCO104 2.0 31.2 1.0
N4 A:NCO104 2.0 30.5 1.0
N3 A:NCO104 2.0 31.6 1.0
O A:HOH339 3.6 41.6 1.0
O A:HOH114 3.9 21.5 1.0
OP2 A:A66 3.9 30.6 1.0
O6 A:G32 4.0 20.4 1.0
O6 A:G31 4.1 16.2 1.0
O A:HOH310 4.1 36.7 1.0
O A:HOH170 4.2 18.1 1.0
O A:HOH278 4.3 31.9 1.0
O A:HOH126 4.3 15.0 1.0
O A:HOH116 4.3 17.9 1.0
N7 A:G31 4.4 15.6 1.0
C6 A:G31 4.9 16.5 1.0
C6 A:G32 5.0 20.0 1.0

Cobalt binding site 5 out of 8 in 2eew

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Cobalt binding site 5 out of 8 in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co105

b:42.2
occ:1.00
 CO A:NCO105 0.0 42.2 1.0
N5 A:NCO105 2.0 38.5 1.0
N6 A:NCO105 2.0 39.3 1.0
N4 A:NCO105 2.0 39.5 1.0
N3 A:NCO105 2.0 38.9 1.0
N1 A:NCO105 2.0 39.4 1.0
N2 A:NCO105 2.0 39.1 1.0
O A:HOH239 3.5 37.9 1.0
O A:HOH142 3.7 28.1 1.0
O A:HOH220 3.9 35.4 1.0
OP2 A:G37 3.9 13.6 1.0
O A:HOH163 4.1 29.3 1.0
O6 A:G38 4.3 20.0 1.0
O A:HOH261 4.3 24.4 1.0
N7 A:G38 4.3 16.9 1.0
N7 A:G37 4.4 17.1 1.0
O A:HOH197 4.5 35.6 1.0
C8 A:G37 5.0 16.9 1.0

Cobalt binding site 6 out of 8 in 2eew

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Cobalt binding site 6 out of 8 in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co109

b:83.5
occ:1.00
 CO A:NCO109 0.0 83.5 1.0
N6 A:NCO109 2.0 83.2 1.0
N1 A:NCO109 2.0 83.2 1.0
N3 A:NCO109 2.0 83.0 1.0
N5 A:NCO109 2.0 83.2 1.0
N2 A:NCO109 2.0 82.8 1.0
N4 A:NCO109 2.0 83.3 1.0
OP1 A:A24 4.2 34.5 1.0
OP2 A:C71 4.3 23.7 1.0
O A:HOH237 4.4 26.0 1.0
O A:HOH294 4.7 34.2 1.0
O A:HOH293 4.8 51.8 1.0
O A:HOH181 4.8 34.4 1.0
O A:HOH203 4.9 34.6 1.0

Cobalt binding site 7 out of 8 in 2eew

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Cobalt binding site 7 out of 8 in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co111

b:0.0
occ:1.00
 CO A:NCO111 0.0 0.0 1.0
N6 A:NCO111 2.0 98.7 1.0
N4 A:NCO111 2.0 98.9 1.0
N5 A:NCO111 2.0 98.6 1.0
N2 A:NCO111 2.0 98.9 1.0
N1 A:NCO111 2.0 98.8 1.0
N3 A:NCO111 2.0 98.6 1.0
O A:HOH210 3.4 31.3 1.0
O A:HOH290 3.8 71.3 1.0
OP2 A:A33 4.0 19.8 1.0
O A:HOH133 4.1 15.6 1.0
OP2 A:G32 4.1 23.3 1.0
O A:HOH192 4.2 42.9 1.0
O A:HOH207 4.2 37.5 1.0
O A:HOH267 4.5 33.5 1.0
O A:HOH127 4.7 25.9 1.0
P A:G32 4.9 20.5 1.0
OP1 A:G32 4.9 22.4 1.0
O A:HOH230 5.0 44.8 1.0

Cobalt binding site 8 out of 8 in 2eew

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Cobalt binding site 8 out of 8 in the Guanine Riboswitch U47C Mutant Bound to Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Guanine Riboswitch U47C Mutant Bound to Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co112

b:49.4
occ:0.64
 CO A:NCO112 0.0 49.4 0.6
N4 A:NCO112 2.0 47.0 0.6
N6 A:NCO112 2.0 47.9 0.6
N2 A:NCO112 2.0 47.5 0.6
N3 A:NCO112 2.0 47.4 0.6
N5 A:NCO112 2.0 47.5 0.6
N1 A:NCO112 2.0 47.4 0.6
O A:HOH317 4.0 50.8 1.0
OP1 A:G72 4.2 19.8 1.0
O A:HOH297 4.8 32.0 1.0
OP2 A:A73 4.8 28.8 1.0
OP1 A:A73 4.9 30.8 1.0

Reference:

S.D.Gilbert, C.E.Love, A.L.Edwards, R.T.Batey. Mutational Analysis of the Purine Riboswitch Aptamer Domain Biochemistry V. 46 13297 2007.
ISSN: ISSN 0006-2960
PubMed: 17960911
DOI: 10.1021/BI700410G
Page generated: Tue Jul 30 15:05:35 2024

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