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Cobalt in PDB 4l81: Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))

Protein crystallography data

The structure of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)), PDB code: 4l81 was solved by J.J.Trausch, F.E.Reyes, A.L.Edwards, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.95
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.930, 120.930, 186.560, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 23.2

Other elements in 4l81:

The structure of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) (pdb code 4l81). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)), PDB code: 4l81:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cobalt binding site 1 out of 9 in 4l81

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Cobalt binding site 1 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:0.5
occ:1.00
CO A:NCO102 0.0 0.5 1.0
N1 A:NCO102 2.0 0.4 1.0
N3 A:NCO102 2.0 0.6 1.0
N4 A:NCO102 2.0 0.6 1.0
N5 A:NCO102 2.0 0.0 1.0
N2 A:NCO102 2.0 0.1 1.0
N6 A:NCO102 2.0 0.6 1.0
OP2 A:A89 2.8 83.3 1.0
O6 A:G91 3.8 71.5 1.0
P A:A89 4.0 81.1 1.0
N7 A:A90 4.2 66.5 1.0
C5' A:G88 4.3 80.9 1.0
O5' A:A89 4.3 79.8 1.0
N1 A:G91 4.3 71.2 1.0
O3' A:G88 4.4 83.2 1.0
C6 A:G91 4.5 71.3 1.0
C4' A:G88 4.5 80.7 1.0
OP2 A:A90 4.5 75.8 1.0
N6 A:A90 4.8 66.7 1.0
N7 A:A89 4.9 68.4 1.0
C8 A:A89 5.0 68.6 1.0

Cobalt binding site 2 out of 9 in 4l81

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Cobalt binding site 2 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:0.8
occ:1.00
CO A:NCO103 0.0 0.8 1.0
N3 A:NCO103 2.0 0.2 1.0
N1 A:NCO103 2.0 0.8 1.0
N2 A:NCO103 2.0 0.3 1.0
N4 A:NCO103 2.0 0.6 1.0
N5 A:NCO103 2.0 0.8 1.0
N6 A:NCO103 2.0 0.3 1.0
O2' A:A43 4.1 78.1 1.0
N1 A:A26 4.1 70.7 1.0
O6 A:G46 4.1 61.4 1.0
N7 A:G46 4.2 64.4 1.0
N1 A:A25 4.2 67.6 1.0
N7 A:G45 4.2 56.6 1.0
O6 A:G45 4.3 56.8 1.0
C2 A:A26 4.4 71.3 1.0
C5 A:G45 4.7 55.8 1.0
C6 A:G45 4.8 56.7 1.0
N6 A:A25 4.8 67.7 1.0
C6 A:G46 4.9 63.7 1.0
C5 A:G46 4.9 63.9 1.0
C2 A:A25 4.9 69.5 1.0
C6 A:A25 5.0 65.8 1.0

Cobalt binding site 3 out of 9 in 4l81

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Cobalt binding site 3 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co104

b:0.1
occ:1.00
CO A:NCO104 0.0 0.1 1.0
N4 A:NCO104 2.0 0.8 1.0
N6 A:NCO104 2.0 0.8 1.0
N5 A:NCO104 2.0 0.7 1.0
N2 A:NCO104 2.0 0.7 1.0
N3 A:NCO104 2.0 0.8 1.0
N1 A:NCO104 2.0 0.8 1.0
O6 A:G58 3.6 99.3 1.0
N7 A:G58 3.7 98.1 1.0
C6 A:G58 4.2 98.7 1.0
C5 A:G58 4.3 98.3 1.0
C8 A:G58 4.7 97.0 1.0
OP2 A:G60 4.9 94.6 1.0

Cobalt binding site 4 out of 9 in 4l81

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Cobalt binding site 4 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co105

b:0.2
occ:1.00
CO A:NCO105 0.0 0.2 1.0
N5 A:NCO105 2.0 0.9 1.0
N3 A:NCO105 2.0 0.7 1.0
N6 A:NCO105 2.0 0.0 1.0
N4 A:NCO105 2.0 0.7 1.0
N1 A:NCO105 2.0 0.1 1.0
N2 A:NCO105 2.0 0.7 1.0
O5' A:C53 4.1 0.5 1.0
O4' A:C53 4.3 0.5 1.0
OP2 A:C53 4.3 0.1 1.0
OP1 A:U50 4.6 93.3 1.0
C4' A:C53 4.9 0.1 1.0
P A:C53 4.9 0.4 1.0

Cobalt binding site 5 out of 9 in 4l81

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Cobalt binding site 5 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co106

b:0.3
occ:1.00
CO A:NCO106 0.0 0.3 1.0
N3 A:NCO106 2.0 1.0 1.0
N5 A:NCO106 2.0 1.0 1.0
N4 A:NCO106 2.0 0.1 1.0
N6 A:NCO106 2.0 0.0 1.0
N1 A:NCO106 2.0 0.9 1.0
N2 A:NCO106 2.0 1.0 1.0
O6 A:G83 4.1 81.2 1.0
N7 A:G83 4.2 78.7 1.0
O6 A:G82 4.4 90.9 1.0
N7 A:G82 4.4 87.4 1.0
C6 A:G83 4.9 80.7 1.0
C6 A:G82 4.9 88.4 1.0
C5 A:G83 4.9 80.1 1.0
C5 A:G82 4.9 87.6 1.0

Cobalt binding site 6 out of 9 in 4l81

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Cobalt binding site 6 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co107

b:0.0
occ:1.00
CO A:NCO107 0.0 0.0 1.0
N4 A:NCO107 2.0 0.6 1.0
N2 A:NCO107 2.0 0.7 1.0
N5 A:NCO107 2.0 0.7 1.0
N3 A:NCO107 2.0 0.6 1.0
N1 A:NCO107 2.0 0.6 1.0
N6 A:NCO107 2.0 0.6 1.0
O6 A:G30 3.9 58.9 1.0
C5 A:U29 4.1 61.9 1.0
O4 A:U29 4.3 61.0 1.0
N7 A:G30 4.3 56.5 1.0
OP2 A:U29 4.4 66.5 1.0
C4 A:U29 4.5 60.4 1.0
MG A:MG112 4.5 81.4 1.0
C6 A:G30 4.7 57.6 1.0
N4 A:C42 4.8 61.2 1.0
OP2 A:C28 4.8 67.7 1.0
O6 A:G31 4.9 64.1 1.0
C5 A:G30 4.9 56.8 1.0
N4 A:C41 4.9 68.6 1.0
C6 A:U29 5.0 61.0 1.0

Cobalt binding site 7 out of 9 in 4l81

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Cobalt binding site 7 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co108

b:0.6
occ:1.00
CO A:NCO108 0.0 0.6 1.0
N4 A:NCO108 2.0 0.2 1.0
N3 A:NCO108 2.0 0.2 1.0
N1 A:NCO108 2.0 0.9 1.0
N5 A:NCO108 2.0 0.2 1.0
N6 A:NCO108 2.0 0.2 1.0
N2 A:NCO108 2.0 0.0 1.0
O6 A:G23 3.6 78.2 1.0
O6 A:G22 3.8 86.9 1.0
N7 A:G22 4.0 88.6 1.0
N4 A:C21 4.5 99.8 1.0
O4 A:U50 4.5 91.8 1.0
C6 A:G22 4.5 87.0 1.0
C6 A:G23 4.6 77.2 1.0
N4 A:C49 4.6 74.5 1.0
C5 A:G22 4.6 87.7 1.0
N7 A:G23 4.8 77.2 1.0
C5 A:C21 4.9 0.6 1.0
C4 A:C21 4.9 0.3 1.0

Cobalt binding site 8 out of 9 in 4l81

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Cobalt binding site 8 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co109

b:0.9
occ:1.00
CO A:NCO109 0.0 0.9 1.0
N3 A:NCO109 2.0 0.6 1.0
N6 A:NCO109 2.0 0.5 1.0
N4 A:NCO109 2.0 0.6 1.0
N2 A:NCO109 2.0 0.3 1.0
N1 A:NCO109 2.0 0.5 1.0
N5 A:NCO109 2.0 0.7 1.0
N7 A:G77 3.9 95.5 1.0
O6 A:G77 4.3 96.8 1.0
OP1 A:G79 4.4 91.4 1.0
C5 A:G77 4.6 95.0 1.0
C8 A:G77 4.7 94.8 1.0
C6 A:G77 4.8 95.3 1.0

Cobalt binding site 9 out of 9 in 4l81

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Cobalt binding site 9 out of 9 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co110

b:0.7
occ:1.00
CO A:NCO110 0.0 0.7 1.0
N4 A:NCO110 2.0 0.5 1.0
N3 A:NCO110 2.0 0.6 1.0
N6 A:NCO110 2.0 0.5 1.0
N1 A:NCO110 2.0 0.4 1.0
N5 A:NCO110 2.0 0.3 1.0
N2 A:NCO110 2.0 0.3 1.0
OP2 A:A26 4.2 74.3 1.0
N7 A:A26 4.2 70.4 1.0
OP2 A:C42 4.4 77.7 1.0
C8 A:A26 4.6 70.5 1.0
OP2 A:A25 4.8 82.6 1.0

Reference:

J.J.Trausch, Z.Xu, A.L.Edwards, F.E.Reyes, P.E.Ross, R.Knight, R.T.Batey. Structural Basis For Diversity in the Sam Clan of Riboswitches. Proc.Natl.Acad.Sci.Usa V. 111 6624 2014.
ISSN: ISSN 0027-8424
PubMed: 24753586
DOI: 10.1073/PNAS.1312918111
Page generated: Sun Dec 13 10:45:08 2020

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