Magnesium in PDB 6n2v: Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)

The structure of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II), PDB code: 6n2v was solved by I.R.Price, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.64 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.296, 85.167, 92.463, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 22.1

The structure of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) also contains other interesting chemical elements:

Strontium	(Sr)	9 atoms
Manganese	(Mn)	7 atoms
Sodium	(Na)	1 atom

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 39;

Binding sites:

The binding sites of Magnesium atom in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) (pdb code 6n2v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 39 binding sites of Magnesium where determined in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II), PDB code: 6n2v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:99.6 occ:1.00 N7 A:G96 4.3 62.7 1.0 O6 A:G97 4.6 64.3 1.0 O6 A:G96 4.7 60.5 1.0 N6 A:A95 4.8 67.0 1.0 N7 A:A95 4.8 67.3 1.0

Magnesium binding site 2 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:89.2 occ:1.00 O6 A:G89 3.5 53.1 1.0 C8 A:G11 4.4 53.4 1.0 O2' A:G11 4.4 56.1 1.0 C2' A:G11 4.6 52.3 1.0 C6 A:G89 4.7 52.4 1.0 OP2 A:G87 4.9 58.2 1.0 N7 A:G11 4.9 59.5 1.0

Magnesium binding site 3 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:67.3 occ:1.00 O6 A:G57 2.2 75.8 1.0 C6 A:G57 3.0 65.8 1.0 N7 A:G57 3.3 61.0 1.0 C5 A:G57 3.5 61.0 1.0 N4 A:C56 4.1 56.2 1.0 N1 A:G57 4.2 60.8 1.0 C8 A:G57 4.6 64.9 1.0 OP1 A:A59 4.6 64.4 1.0 C4 A:C56 4.6 58.9 1.0 C5 A:C56 4.8 60.7 1.0 C4 A:G57 4.8 60.1 1.0 OP2 A:A59 5.0 61.8 1.0

Magnesium binding site 4 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:77.3 occ:1.00 OP2 A:A10 2.0 47.6 1.0 P A:A10 3.4 47.5 1.0 O3' A:G9 3.8 53.1 1.0 OP1 A:G7 4.2 69.8 1.0 OP2 A:G8 4.2 53.7 1.0 OP1 A:A10 4.4 54.4 1.0 O5' A:A10 4.4 44.9 1.0 C5' A:A10 4.4 50.7 1.0 O2' A:G9 4.5 55.4 1.0 O2' A:C44 4.7 44.0 1.0 O3' A:A10 4.9 48.2 1.0 O5' A:G11 4.9 41.5 1.0 C4' A:A10 4.9 47.1 1.0

Magnesium binding site 5 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:98.4 occ:1.00 OP1 A:G72 3.4 83.5 1.0 P A:G72 4.2 76.0 1.0 O3' A:A71 4.4 68.2 1.0 OP2 A:G72 4.4 66.2 1.0 OP1 A:A71 4.7 61.9 1.0 C5' A:A71 5.0 54.0 1.0

Magnesium binding site 6 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:86.4 occ:1.00 OP2 A:A78 3.4 54.1 1.0 OP1 A:A78 3.5 61.4 1.0 P A:A78 3.7 63.1 1.0 OP1 A:G77 3.9 66.9 1.0 O3' A:G77 3.9 62.5 1.0 C5' A:G77 4.4 60.9 1.0 O5' A:G77 4.8 64.6 1.0 C3' A:G77 4.9 62.3 1.0 C4' A:G77 4.9 57.6 1.0 P A:G77 5.0 61.2 1.0

Magnesium binding site 7 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:0.3 occ:1.00 OP2 A:G61 3.8 58.5 1.0 OP1 A:G61 4.4 65.5 1.0 P A:G61 4.6 60.0 1.0

Magnesium binding site 8 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:0.3 occ:1.00 OP2 A:C99 2.3 76.2 1.0 P A:C99 3.6 78.1 1.0 OP1 A:C99 4.3 81.7 1.0 OP1 A:C98 4.4 76.8 1.0 O3' A:C98 4.4 78.7 1.0 O5' A:C98 4.4 63.0 1.0 O5' A:C99 4.7 77.4 1.0 C3' A:C98 4.7 70.6 1.0 P A:C98 4.8 77.9 1.0 C5' A:C98 4.9 64.0 1.0 OP2 A:C98 5.0 68.5 1.0

Magnesium binding site 9 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:96.5 occ:1.00 O6 A:G81 3.3 68.1 1.0 MG A:MG111 3.5 86.6 1.0 N7 A:G81 4.0 67.5 1.0 C6 A:G81 4.2 67.6 1.0 C5 A:G81 4.4 67.3 1.0 O6 A:G82 4.8 71.3 1.0

Magnesium binding site 10 out of 39 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:89.0 occ:1.00 OP1 A:A79 2.3 64.8 1.0 O6 A:G77 2.4 71.0 1.0 C6 A:G77 2.9 61.7 1.0 P A:A79 3.4 63.7 1.0 C5 A:G77 3.5 61.1 1.0 OP2 A:A79 3.6 62.5 1.0 N1 A:G77 3.7 55.7 1.0 N7 A:G77 3.8 59.0 1.0 O5' A:A79 4.5 61.2 1.0 C4 A:G77 4.5 61.2 1.0 O3' A:A78 4.5 56.6 1.0 C2 A:G77 4.7 61.6 1.0 C8 A:G77 4.8 61.2 1.0

K.C.Suddala, I.R.Price, S.S.Dandpat, M.Janecek, P.Kuhrova, J.Sponer, P.Banas, A.Ke, N.G.Walter. Local-to-Global Signal Transduction at the Core of A MN2+Sensing Riboswitch. Nat Commun V. 10 4304 2019.
ISSN: ESSN 2041-1723
PubMed: 31541094
DOI: 10.1038/S41467-019-12230-5