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

Protein crystallography data

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

Other elements in 6n2v:

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

Magnesium (Mg) 39 atoms
Manganese (Mn) 7 atoms
Sodium (Na) 1 atom

Strontium Binding Sites:

The binding sites of Strontium 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 Strontium atom.
In total 9 binding sites of Strontium where determined in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II), PDB code: 6n2v:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Strontium binding site 1 out of 9 in 6n2v

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Strontium binding site 1 out of 9 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr120

b:61.5
occ:1.00
 O A:HOH201 2.4 63.1 1.0
O A:HOH203 2.4 69.2 1.0
O A:HOH202 2.4 66.6 1.0
O4 A:U43 2.5 48.9 1.0
O6 A:G66 2.5 53.7 1.0
C6 A:G66 3.7 49.3 1.0
C4 A:U43 3.7 43.0 1.0
N4 A:C44 4.2 45.5 1.0
O4 A:U65 4.2 46.5 1.0
O6 A:G67 4.3 45.2 1.0
N6 A:A42 4.3 49.0 1.0
N3 A:U43 4.5 43.7 1.0
C5 A:G66 4.5 54.5 1.0
N7 A:G66 4.6 53.3 1.0
N1 A:G66 4.7 43.8 1.0
C5 A:U43 4.8 46.7 1.0
C4 A:U65 5.0 55.6 1.0

Strontium binding site 2 out of 9 in 6n2v

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Strontium binding site 2 out of 9 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr121

b:0.2
occ:1.00
 O4 A:U68 3.3 49.5 1.0
O4 A:U41 4.0 51.7 1.0
C4 A:U68 4.1 46.1 1.0
O6 A:G40 4.1 53.0 1.0
C5 A:U68 4.5 42.3 1.0
O6 A:G69 4.6 49.0 1.0
N6 A:A42 4.8 49.0 1.0
N4 A:C70 5.0 46.6 1.0

Strontium binding site 3 out of 9 in 6n2v

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Strontium binding site 3 out of 9 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr122

b:0.1
occ:1.00
 O6 A:G8 2.4 71.5 1.0
C6 A:G8 3.5 71.0 1.0
N7 A:G7 4.4 71.6 1.0
C5 A:G8 4.4 68.6 1.0
OP2 A:G7 4.4 57.9 1.0
N1 A:G8 4.5 70.8 1.0
N7 A:G8 4.5 64.8 1.0
N7 A:G6 4.7 61.7 1.0
O5' A:A90 4.8 64.5 1.0
C8 A:G6 4.9 66.5 1.0

Strontium binding site 4 out of 9 in 6n2v

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Strontium binding site 4 out of 9 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr123

b:78.7
occ:1.00
 OP1 A:G8 2.4 70.8 1.0
OP1 A:A46 2.4 54.4 1.0
OP1 A:A10 2.4 54.4 1.0
OP2 A:G9 2.4 62.3 1.0
P A:G8 3.6 49.3 1.0
P A:A46 3.7 50.6 1.0
P A:A10 3.9 47.5 1.0
P A:G9 3.9 62.3 1.0
O5' A:G8 4.0 51.9 1.0
C5' A:G8 4.0 57.8 1.0
OP2 A:G8 4.2 53.7 1.0
OP2 A:A46 4.3 57.0 1.0
C3' A:G9 4.3 55.2 1.0
C5' A:A46 4.4 52.4 1.0
O5' A:A46 4.5 51.9 1.0
OP1 A:G9 4.6 56.2 1.0
O3' A:G9 4.6 53.1 1.0
O5' A:A10 4.7 44.9 1.0
O3' A:G8 4.7 58.0 1.0
OP2 A:A10 4.7 47.6 1.0
C5' A:A45 4.8 41.3 1.0
O5' A:G9 4.8 61.1 1.0
O3' A:A45 4.8 53.5 1.0
C3' A:A45 4.8 48.8 1.0
O3' A:G7 4.8 62.4 1.0
OP1 A:A45 4.9 43.6 1.0
C4' A:A45 5.0 46.3 1.0

Strontium binding site 5 out of 9 in 6n2v

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Strontium binding site 5 out of 9 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr124

b:0.1
occ:1.00
 O2 A:C47 2.4 70.8 1.0
O B:HOH203 2.9 71.9 1.0
C2 A:C47 3.6 56.4 1.0
N3 A:C47 4.3 52.9 1.0
O2' B:A92 4.4 60.0 1.0
N1 A:C47 4.6 56.7 1.0
O2' A:C47 4.7 73.2 1.0
C1' A:C47 4.7 65.1 1.0
C2' A:C47 4.9 65.6 1.0

Strontium binding site 6 out of 9 in 6n2v

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Strontium binding site 6 out of 9 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr125

b:87.0
occ:1.00
 N7 A:G25 2.5 61.8 1.0
C8 A:G25 3.3 59.4 1.0
C5 A:G25 3.5 57.8 1.0
O6 A:G25 3.8 63.9 1.0
C6 A:G25 4.1 58.2 1.0
N7 A:G24 4.1 64.4 1.0
OP1 A:A27 4.2 55.0 1.0
OP2 A:A27 4.3 54.7 1.0
N9 A:G25 4.5 53.1 1.0
C8 A:G24 4.6 65.9 1.0
OP2 A:G24 4.6 67.1 1.0
C4 A:G25 4.6 54.0 1.0
OP2 A:G25 4.7 64.8 1.0
C5 A:G24 4.8 63.4 1.0
P A:A27 4.8 52.6 1.0

Strontium binding site 7 out of 9 in 6n2v

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Strontium binding site 7 out of 9 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr129

b:78.5
occ:1.00
 O6 B:G8 2.4 55.8 1.0
C6 B:G8 3.5 49.5 1.0
C5 B:G8 4.3 48.8 1.0
OP2 B:G7 4.4 46.5 1.0
N7 B:G8 4.4 54.7 1.0
N1 B:G8 4.5 52.0 1.0
N7 B:G7 4.5 48.7 1.0
C5' B:A90 4.6 56.7 1.0
N7 B:G9 4.8 53.3 1.0
OP2 B:G6 4.8 58.5 1.0
O5' B:A90 4.9 54.8 1.0

Strontium binding site 8 out of 9 in 6n2v

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Strontium binding site 8 out of 9 in the Manganese Riboswitch From Xanthmonas Oryzae Bound to Mn(II)


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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
B:Sr130

b:87.6
occ:1.00
 O6 B:G66 2.4 55.7 1.0
O4 B:U43 2.5 54.0 1.0
C6 B:G66 3.6 48.0 1.0
C4 B:U43 3.7 46.6 1.0
O6 B:G67 4.0 46.3 1.0
N4 B:C44 4.2 41.7 1.0
N3 B:U43 4.4 44.5 1.0
N6 B:A42 4.4 48.6 1.0
C5 B:G66 4.4 51.4 1.0
N7 B:G66 4.5 58.1 1.0
N1 B:G66 4.6 47.0 1.0
O4 B:U65 4.6 51.6 1.0
C5 B:U43 4.8 51.5 1.0

Strontium binding site 9 out of 9 in 6n2v

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


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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
B:Sr131

b:0.0
occ:1.00
 O6 B:G97 4.0 58.0 1.0
N7 B:G96 4.7 53.3 1.0
O6 B:G96 4.8 57.8 1.0
N7 B:A95 5.0 56.9 1.0
N6 B:A95 5.0 52.9 1.0
C6 B:G97 5.0 55.6 1.0
N7 B:G97 5.0 53.2 1.0

Reference:

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
Page generated: Fri Oct 11 06:42:37 2024

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