Strontium in PDB 4y1m: An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State

The structure of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State, PDB code: 4y1m 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)	123.60 / 3.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	159.384, 159.384, 277.108, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 25.2

The structure of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 65;

Binding sites:

The binding sites of Strontium atom in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State (pdb code 4y1m). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 65 binding sites of Strontium where determined in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State, PDB code: 4y1m:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr201 b:80.3 occ:0.98 OP1 B:G9 2.4 0.4 1.0 OP2 B:G10 2.4 71.6 1.0 OP1 B:U49 2.4 83.8 1.0 OP1 B:A45 2.4 0.7 1.0 OP1 B:A11 2.5 98.8 1.0 P B:G9 3.6 81.6 1.0 P B:A11 3.8 73.8 1.0 P B:A45 3.8 74.1 1.0 O5' B:G9 3.9 66.4 1.0 P B:U49 3.9 77.1 1.0 P B:G10 3.9 73.2 1.0 C5' B:G9 4.0 72.0 1.0 C3' B:G10 4.3 76.3 1.0 OP2 B:G9 4.4 62.8 1.0 OP2 B:A11 4.4 78.1 1.0 OP2 B:A45 4.4 86.5 1.0 C5' B:A45 4.5 72.8 1.0 O3' B:G10 4.6 63.8 1.0 O5' B:G10 4.6 83.7 1.0 O3' B:U48 4.7 78.8 1.0 O5' B:A45 4.7 0.6 1.0 C5' B:A44 4.7 65.1 1.0 O3' B:G9 4.8 97.9 1.0 OP2 B:U49 4.8 71.1 1.0 O5' B:U49 4.8 86.8 1.0 C3' B:A44 4.8 71.4 1.0 OP1 B:G10 4.8 96.2 1.0 C5' B:U49 4.8 0.2 1.0 C4' B:A44 4.9 65.2 1.0 O3' B:A44 4.9 58.2 1.0 O3' B:G8 4.9 89.6 1.0 O B:HOH322 4.9 83.2 1.0 O5' B:A11 4.9 75.1 1.0 C5' B:G10 5.0 72.5 1.0

Strontium binding site 2 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr202 b:1.0 occ:1.00 O6 B:G25 2.4 0.6 1.0 O B:HOH337 3.0 0.9 1.0 C6 B:G25 3.5 0.5 1.0 N4 B:C24 3.9 79.1 1.0 C5 B:G25 4.3 94.5 1.0 N7 B:G25 4.3 0.8 1.0 N1 B:G25 4.5 83.9 1.0 C4 B:C24 4.6 84.1 1.0 C5 B:C24 4.7 0.2 1.0 OP1 B:A27 4.9 0.5 1.0

Strontium binding site 3 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr203 b:1.0 occ:1.00 O4 B:U34 2.4 0.2 1.0 O B:HOH345 3.1 0.3 1.0 C4 B:U34 3.5 84.8 1.0 C5 B:U34 4.0 0.7 1.0 N7 B:A33 4.2 88.6 1.0 N6 B:A33 4.2 94.7 1.0 N6 B:A19 4.5 95.5 1.0 N3 B:U34 4.7 76.3 1.0 C5 B:A33 4.8 82.5 1.0 C6 B:A33 4.9 84.9 1.0

Strontium binding site 4 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr204 b:86.5 occ:1.00 O6 B:G65 2.4 80.9 1.0 O B:HOH311 2.4 83.3 1.0 O4 B:U42 3.3 89.3 1.0 C6 B:G65 3.6 70.7 1.0 O4 B:U64 4.0 81.3 1.0 N4 B:C43 4.0 84.2 1.0 O6 B:G66 4.4 0.1 1.0 C5 B:G65 4.4 69.9 1.0 O6 B:G41 4.5 0.9 1.0 N7 B:G65 4.6 85.6 1.0 C4 B:U42 4.6 67.7 1.0 N1 B:G65 4.6 76.1 1.0 C4 B:U64 4.8 59.0 1.0 SR B:SR232 4.8 0.1 1.0

Strontium binding site 5 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr205 b:0.8 occ:1.00 O B:HOH315 2.4 0.0 1.0 O6 B:G9 2.4 0.4 1.0 C6 B:G9 3.6 92.5 1.0 O B:HOH316 4.2 0.4 1.0 C5 B:G9 4.5 75.8 1.0 SR B:SR236 4.5 0.0 1.0 N1 B:G9 4.5 83.0 1.0 N7 B:G9 4.6 0.9 1.0 N7 B:G10 4.7 61.6 1.0 N7 B:G8 4.8 73.2 1.0 O5' B:A98 4.8 90.5 1.0

Strontium binding site 6 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr206 b:93.0 occ:1.00 OP2 B:U48 2.4 92.6 1.0 OP1 B:G10 2.4 96.2 1.0 OP1 B:C46 2.4 92.5 1.0 P B:C46 3.6 79.3 1.0 P B:U48 3.7 81.1 1.0 O3' B:A45 3.7 0.5 1.0 P B:G10 3.7 73.2 1.0 O3' B:G9 4.1 97.9 1.0 OP1 B:U48 4.2 0.8 1.0 O5' B:G10 4.2 83.7 1.0 O5' B:U48 4.5 0.2 1.0 C5' B:G10 4.5 72.5 1.0 OP2 B:C46 4.6 86.3 1.0 O4' B:U48 4.7 86.2 1.0 O5' B:C46 4.7 98.1 1.0 C5' B:U48 4.8 0.7 1.0 C4' B:U48 4.8 0.2 1.0 C5' B:C46 4.8 86.9 1.0 O3' B:A47 4.9 86.9 1.0 C3' B:A47 4.9 80.1 1.0 O2' B:U13 4.9 0.6 1.0 OP2 B:G10 5.0 71.6 1.0

Strontium binding site 7 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr207 b:0.8 occ:1.00 OP2 B:A59 4.6 0.7 1.0 O B:HOH354 5.0 70.6 1.0 N1 B:G56 5.0 20.0 1.0

Strontium binding site 8 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr208 b:0.5 occ:0.85 N7 B:G94 3.1 86.2 1.0 O6 B:G94 3.4 95.9 1.0 C5 B:G94 3.9 84.2 1.0 C6 B:G94 4.0 90.9 1.0 O6 B:G18 4.0 0.2 1.0 C8 B:G94 4.2 84.2 1.0 C6 B:G18 4.7 92.5 1.0 O6 B:G95 4.8 80.9 1.0 N1 B:G18 4.9 88.2 1.0

Strontium binding site 9 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr209 b:0.9 occ:1.00 N7 B:A11 4.3 0.7 1.0 OP2 B:U13 4.5 0.8 1.0 O2' B:G66 4.6 69.6 1.0 O3' B:G66 4.7 79.3 1.0 OP1 B:U13 4.8 64.2 1.0 C8 B:A11 4.9 93.7 1.0 C4' B:G66 4.9 75.6 1.0

Strontium binding site 10 out of 65 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Sr210 b:0.2 occ:0.97 O B:HOH335 2.4 98.2 1.0 O B:HOH307 2.4 0.7 1.0 OP2 B:A11 3.8 78.1 1.0 O B:HOH322 4.1 83.2 1.0 OP1 B:G8 4.2 0.5 1.0 OP2 B:G9 4.5 62.8 1.0 OP1 B:A44 4.5 88.1 1.0 O3' B:C43 4.6 62.4 1.0 O B:HOH312 4.7 96.3 1.0 C5' B:G8 4.9 87.2 1.0

I.R.Price, A.Gaballa, F.Ding, J.D.Helmann, A.Ke. Mn(2+)-Sensing Mechanisms of Yybp-Ykoy Orphan Riboswitches. Mol.Cell V. 57 1110 2015.
ISSN: ISSN 1097-2765
PubMed: 25794619
DOI: 10.1016/J.MOLCEL.2015.02.016