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Magnesium in PDB 3la5: X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine

Protein crystallography data

The structure of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine, PDB code: 3la5 was solved by M.S.Dunstan, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.08 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.845, 125.105, 24.990, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine (pdb code 3la5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine, PDB code: 3la5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3la5

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Magnesium binding site 1 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:14.2
occ:1.00
 OP1 A:A24 2.1 13.6 1.0
O A:HOH105 2.1 11.2 1.0
O A:HOH120 2.2 14.5 1.0
O A:HOH113 2.2 12.5 1.0
O A:HOH108 2.2 12.9 1.0
O A:HOH109 2.3 12.5 1.0
P A:A24 3.5 13.4 1.0
O A:HOH308 4.0 12.1 1.0
O A:HOH90 4.0 19.4 1.0
O5' A:A24 4.0 11.9 1.0
O A:HOH385 4.0 22.7 1.0
O A:HOH450 4.0 21.3 1.0
O A:HOH141 4.1 30.2 1.0
O A:HOH128 4.1 24.4 1.0
N7 A:A24 4.2 10.8 1.0
C8 A:A24 4.2 13.3 1.0
N7 A:G72 4.3 14.5 1.0
O6 A:G72 4.4 10.2 1.0
OP2 A:A24 4.4 15.7 1.0
O3' A:A23 4.4 13.2 1.0
O A:HOH288 4.4 16.5 1.0
O A:HOH424 4.5 16.4 1.0
O A:HOH453 4.6 15.3 1.0
O A:HOH200 4.7 30.5 1.0
O A:HOH333 4.7 33.6 1.0

Magnesium binding site 2 out of 10 in 3la5

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Magnesium binding site 2 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:14.8
occ:1.00
 O A:HOH395 2.2 12.8 1.0
O A:HOH442 2.2 15.0 1.0
O A:HOH117 2.2 14.9 1.0
O A:HOH118 2.3 13.3 1.0
O A:HOH351 3.9 11.9 1.0
O2' A:A45 4.1 11.9 1.0
O A:HOH449 4.2 22.4 1.0
O A:HOH89 4.3 24.9 1.0
O A:HOH419 4.3 14.9 1.0
N3 A:A45 4.4 9.4 1.0
O A:HOH211 4.6 28.1 1.0
O4' A:G46 4.8 12.1 1.0
C2' A:A45 4.8 10.9 1.0
C2 A:A45 5.0 9.6 1.0

Magnesium binding site 3 out of 10 in 3la5

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Magnesium binding site 3 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3

b:14.4
occ:1.00
 O A:HOH106 2.2 11.9 1.0
O A:HOH114 2.2 13.0 1.0
O A:HOH382 2.2 16.1 1.0
O A:HOH104 2.2 10.5 1.0
O A:HOH356 2.2 10.7 1.0
O A:HOH110 2.3 11.3 1.0
O A:HOH12 4.0 11.8 1.0
O A:HOH437 4.1 17.8 1.0
O6 A:G44 4.1 9.9 1.0
O A:HOH426 4.2 17.1 1.0
N7 A:G43 4.2 12.8 1.0
O A:HOH289 4.2 16.7 1.0
O A:HOH254 4.3 31.2 1.0
O6 A:G43 4.3 11.9 1.0
O A:HOH192 4.3 23.1 1.0
O A:HOH420 4.3 20.8 1.0
O A:HOH237 4.4 24.6 1.0
N7 A:G44 4.4 12.1 1.0
O A:HOH348 4.4 13.7 1.0
C5 A:G43 4.8 10.7 1.0
O A:HOH267 4.8 31.6 1.0
C6 A:G43 4.8 12.3 1.0
C6 A:G44 5.0 10.9 1.0

Magnesium binding site 4 out of 10 in 3la5

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Magnesium binding site 4 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4

b:23.8
occ:1.00
 OP2 A:A23 2.1 20.9 1.0
OP2 A:A24 2.2 15.7 1.0
O A:HOH128 2.3 24.4 1.0
O A:HOH200 2.4 30.5 1.0
O A:HOH410 2.5 36.5 1.0
O A:HOH416 2.5 21.6 1.0
P A:A23 3.3 19.4 1.0
P A:A24 3.4 13.4 1.0
O5' A:A23 3.8 17.5 1.0
O3' A:U22 3.8 17.0 1.0
O A:HOH132 3.9 23.0 1.0
C5' A:A23 3.9 17.9 1.0
OP1 A:A24 3.9 13.6 1.0
O A:HOH177 4.1 35.8 1.0
O A:HOH333 4.3 33.6 1.0
O3' A:A23 4.4 13.2 1.0
O A:HOH109 4.5 12.5 1.0
O A:HOH131 4.5 26.9 1.0
O A:HOH359 4.5 37.4 1.0
O5' A:A24 4.5 11.9 1.0
OP1 A:A23 4.6 20.6 1.0
C3' A:A23 4.6 14.8 1.0
O A:HOH141 4.6 30.2 1.0
C4' A:A23 4.8 19.0 1.0
C8 A:A24 4.9 13.3 1.0
C5' A:A24 4.9 11.9 1.0

Magnesium binding site 5 out of 10 in 3la5

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Magnesium binding site 5 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5

b:49.7
occ:1.00
 OP1 A:U68 1.8 23.1 1.0
O A:HOH147 2.1 24.1 1.0
O A:HOH378 2.2 35.0 1.0
O A:HOH155 2.2 28.5 1.0
O A:HOH435 2.3 26.9 1.0
P A:U68 3.3 21.4 1.0
O3' A:C67 3.8 22.2 1.0
O5' A:U68 4.2 18.8 1.0
OP1 A:C26 4.2 18.3 1.0
OP1 A:C27 4.2 13.8 1.0
OP2 A:U68 4.2 20.1 1.0
C5' A:U68 4.3 18.3 1.0
OP2 A:C27 4.4 13.8 1.0
O A:HOH381 4.4 36.0 1.0
O A:HOH268 4.5 36.7 1.0
O A:HOH367 4.6 37.0 1.0
P A:C27 4.7 12.6 1.0
O A:HOH232 4.9 32.8 1.0

Magnesium binding site 6 out of 10 in 3la5

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Magnesium binding site 6 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6

b:15.3
occ:1.00
 OP1 A:C51 2.1 10.5 1.0
O A:HOH107 2.2 13.8 1.0
O A:HOH116 2.2 16.0 1.0
O A:HOH374 2.3 15.8 1.0
P A:C51 3.4 12.4 1.0
O5' A:C51 4.0 11.1 1.0
C5' A:C51 4.1 10.3 1.0
O A:HOH394 4.2 23.0 1.0
O A:HOH157 4.2 31.0 1.0
O A:HOH446 4.3 21.1 1.0
OP2 A:C51 4.4 11.8 1.0
O3' A:C50 4.4 12.8 1.0
OP2 A:A52 4.5 12.5 1.0

Magnesium binding site 7 out of 10 in 3la5

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Magnesium binding site 7 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:26.8
occ:1.00
 OP1 A:A23 2.2 20.6 1.0
O A:HOH143 2.3 27.1 1.0
O A:HOH165 2.3 21.2 1.0
O A:HOH160 2.4 31.2 1.0
O A:HOH127 2.4 23.5 1.0
O A:HOH241 2.5 32.8 1.0
P A:A23 3.6 19.4 1.0
O A:HOH177 4.1 35.8 1.0
O A:HOH261 4.1 35.0 1.0
O A:HOH429 4.3 28.2 1.0
OP2 A:A23 4.3 20.9 1.0
O5' A:A23 4.3 17.5 1.0
OP2 A:A21 4.4 23.1 1.0
C3' A:U22 4.5 15.1 1.0
O3' A:U22 4.6 17.0 1.0
OP2 A:U22 4.6 18.6 1.0
O A:HOH270 4.7 31.6 1.0
C5' A:A23 4.8 17.9 1.0
O A:HOH256 4.8 34.2 1.0
C5' A:U22 4.8 14.0 1.0
C4' A:U22 4.9 14.7 1.0
O A:HOH359 5.0 37.4 1.0

Magnesium binding site 8 out of 10 in 3la5

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Magnesium binding site 8 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg8

b:33.6
occ:1.00
 O A:HOH440 2.4 29.6 1.0
O A:HOH215 2.5 33.1 1.0
O A:HOH243 2.6 35.4 1.0
O A:HOH461 2.7 25.6 1.0
O A:HOH95 2.7 37.9 1.0
O A:HOH212 2.9 33.3 1.0
O A:HOH400 3.3 32.6 1.0
OP1 A:G46 4.3 19.5 1.0
OP2 A:C47 4.3 13.4 1.0
OP1 A:C47 4.4 19.3 1.0
O A:HOH175 4.5 32.2 1.0
O A:HOH405 4.5 38.0 1.0
P A:C47 4.9 14.6 1.0

Magnesium binding site 9 out of 10 in 3la5

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Magnesium binding site 9 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg10

b:30.1
occ:1.00
 O A:HOH364 2.7 30.1 1.0
O2' A:G38 2.8 15.3 1.0
N2 A:G32 3.0 15.0 1.0
N1 A:A33 3.5 15.3 1.0
C6 A:A33 3.6 14.6 1.0
N6 A:A33 3.7 14.8 1.0
N7 A:A66 3.8 13.1 1.0
N1 A:G32 3.9 16.0 1.0
C2 A:G32 3.9 17.1 1.0
C2' A:G38 4.0 14.0 1.0
O A:HOH203 4.1 27.9 1.0
C2 A:A33 4.2 14.6 1.0
C1' A:G38 4.3 12.2 1.0
C4' A:G38 4.3 14.2 1.0
N6 A:A66 4.3 14.7 1.0
O A:HOH272 4.4 32.0 1.0
C5 A:A33 4.4 13.7 1.0
C5 A:A66 4.4 14.8 1.0
O4' A:G38 4.4 12.9 1.0
C8 A:A66 4.6 20.0 1.0
C5 A:U39 4.6 11.7 1.0
O A:HOH181 4.6 31.2 1.0
O3' A:G38 4.6 12.4 1.0
C3' A:G38 4.6 14.6 1.0
C6 A:A66 4.7 15.2 1.0
C4 A:A33 4.9 15.2 1.0
N3 A:A33 4.9 13.2 1.0

Magnesium binding site 10 out of 10 in 3la5

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Magnesium binding site 10 out of 10 in the X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of X-Ray Crystal Structure of MC6 Rna Riboswitch Bound to Azacytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg11

b:31.9
occ:1.00
 OP1 A:G44 2.2 14.3 1.0
O A:HOH412 2.3 38.8 1.0
O A:HOH411 2.3 22.2 1.0
O A:HOH302 2.4 29.1 1.0
P A:G44 3.5 11.5 1.0
OP2 A:G44 4.0 12.2 1.0
O5' A:G44 4.2 11.1 1.0
O A:HOH250 4.3 41.4 1.0
C5' A:G44 4.6 10.5 1.0
O3' A:G43 4.6 11.3 1.0
O A:HOH418 4.8 15.1 1.0
OP2 A:A45 4.9 21.7 1.0

Reference:

N.Dixon, J.N.Duncan, T.Geerlings, M.S.Dunstan, J.E.G.Mccarthy, D.Leys, J.Micklefield. Reengineering Orthogonally Selective Riboswitches Proc.Natl.Acad.Sci.Usa V. 107 2830 2010.
ISSN: ISSN 0027-8424
PubMed: 20133756
DOI: 10.1073/PNAS.0911209107
Page generated: Wed Aug 14 18:29:08 2024

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