Manganese 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
Magnesium	(Mg)	39 atoms
Sodium	(Na)	1 atom

The binding sites of Manganese 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 Manganese atom.
In total 7 binding sites of Manganese where determined in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II), PDB code: 6n2v:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn118 b:63.7 occ:1.00 OP2 A:A46 2.2 57.0 1.0 N1 A:A48 2.2 71.2 1.0 OP2 A:C47 2.2 48.3 1.0 C6 A:A48 3.1 64.0 1.0 C2 A:A48 3.1 71.4 1.0 N6 A:A48 3.2 60.8 1.0 P A:A46 3.5 50.6 1.0 P A:C47 3.6 56.4 1.0 O5' A:A46 4.0 51.9 1.0 OP1 A:C47 4.2 59.9 1.0 C5' A:A46 4.3 52.4 1.0 OP1 A:A46 4.3 54.4 1.0 C5 A:A48 4.4 61.1 1.0 N3 A:A48 4.4 67.9 1.0 O5' A:C47 4.4 59.0 1.0 OP1 A:G9 4.4 56.2 1.0 O3' A:A46 4.6 58.2 1.0 O3' A:A45 4.6 53.5 1.0 C4 A:A48 4.8 64.7 1.0 C5 A:C47 4.9 53.3 1.0 C3' A:A46 4.9 49.8 1.0 OP2 A:C51 4.9 76.5 1.0

Manganese binding site 2 out of 7 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn119 b:0.6 occ:1.00 OP2 A:C88 3.7 70.5 1.0 O6 A:G11 3.8 59.6 1.0 N7 A:G89 3.9 50.6 1.0 N7 A:G11 3.9 59.5 1.0 C6 A:G11 4.4 54.8 1.0 OP2 A:G89 4.4 52.8 1.0 C5 A:G11 4.4 58.1 1.0 P A:C88 4.6 62.3 1.0 O6 A:G89 4.6 53.1 1.0 C8 A:G89 4.8 50.2 1.0 OP1 A:C88 4.8 62.3 1.0 C5 A:G89 4.9 52.6 1.0 C8 A:G11 4.9 53.4 1.0 O5' A:C88 5.0 51.5 1.0

Manganese binding site 3 out of 7 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 B:Mn101 b:0.8 occ:1.00 O6 B:G18 3.2 92.8 1.0 O4 B:U17 3.6 83.4 1.0 O6 B:G34 3.9 0.8 1.0 N4 B:C35 4.1 0.1 1.0 C6 B:G18 4.4 89.3 1.0 C4 B:U17 4.5 82.8 1.0 N4 B:C19 4.6 93.1 1.0 C5 B:U17 5.0 85.6 1.0

Manganese binding site 4 out of 7 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 B:Mn102 b:57.2 occ:1.00 OP2 B:C47 2.1 54.6 1.0 OP2 B:U52 2.2 56.8 1.0 OP1 B:G9 2.3 48.0 1.0 OP2 B:A46 2.3 52.1 1.0 OP1 B:C51 2.3 61.4 1.0 N7 B:A48 2.3 57.0 1.0 C8 B:A48 3.2 61.4 1.0 C5 B:A48 3.3 57.4 1.0 P B:G9 3.4 52.3 1.0 P B:U52 3.4 54.6 1.0 P B:C51 3.5 61.4 1.0 P B:A46 3.5 43.0 1.0 P B:C47 3.5 47.9 1.0 N6 B:A48 3.5 54.4 1.0 OP2 B:G9 3.7 55.3 1.0 OP1 B:A46 3.8 44.2 1.0 C6 B:A48 3.8 58.3 1.0 OP1 B:U52 3.8 59.5 1.0 O5' B:C51 3.9 58.2 1.0 OP2 B:C51 4.0 55.5 1.0 O3' B:G8 4.2 48.8 1.0 O5' B:C47 4.3 53.6 1.0 C5' B:C51 4.3 56.0 1.0 OP1 B:C47 4.4 45.0 1.0 C5' B:A46 4.4 46.1 1.0 N9 B:A48 4.4 62.8 1.0 C4 B:A48 4.4 57.8 1.0 O5' B:A46 4.4 46.1 1.0 O3' B:A46 4.4 55.8 1.0 MG B:MG115 4.4 46.8 1.0 O3' B:C51 4.5 53.3 1.0 O5' B:U52 4.5 58.0 1.0 O3' B:A45 4.6 46.8 1.0 C3' B:A46 4.6 52.0 1.0 O5' B:G9 4.7 47.3 1.0 O3' B:A50 4.8 60.1 1.0 C3' B:C51 4.9 62.3 1.0

Manganese binding site 5 out of 7 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 B:Mn103 b:0.5 occ:1.00 O6 B:G57 2.1 81.0 1.0 MG B:MG122 2.2 1.0 1.0 C6 B:G57 3.2 71.5 1.0 N7 B:G57 3.7 73.8 1.0 C5 B:G57 3.8 71.8 1.0 OP2 B:C56 4.3 68.8 1.0 N1 B:G57 4.4 64.6 1.0 C5 B:C56 4.6 67.9 1.0 N4 B:C56 4.9 65.1 1.0 C8 B:G57 4.9 70.1 1.0

Manganese binding site 6 out of 7 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 B:Mn126 b:0.3 occ:1.00 N7 B:G25 2.4 85.9 1.0 C5 B:G25 3.3 84.7 1.0 O6 B:G25 3.3 86.5 1.0 C8 B:G25 3.4 84.6 1.0 C6 B:G25 3.6 85.0 1.0 OP1 B:A27 4.1 70.4 1.0 N7 B:G24 4.3 89.4 1.0 C4 B:G25 4.5 82.6 1.0 OP2 B:A27 4.5 79.0 1.0 N9 B:G25 4.5 81.8 1.0 C5 B:G24 4.6 89.5 1.0 O6 B:G24 4.7 85.0 1.0 C6 B:G24 4.8 89.8 1.0 C8 B:G24 4.9 91.1 1.0 P B:A27 4.9 75.0 1.0 N1 B:G25 4.9 82.9 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 B:Mn127 b:0.5 occ:1.00 O4 B:U83 3.4 92.6 1.0 O6 B:G72 4.0 78.7 1.0 N6 B:A74 4.2 82.4 1.0 O6 B:G73 4.2 91.6 1.0 C4 B:U83 4.6 96.4 1.0 C6 B:G72 4.8 77.2 1.0 O6 B:G82 4.9 70.0 1.0 N7 B:G72 4.9 81.8 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