Strontium in PDB 4y1j: Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+

The structure of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+, PDB code: 4y1j 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)	47.40 / 2.24
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.419, 62.510, 69.969, 116.21, 101.83, 98.83
R / Rfree (%)	19.9 / 24.2

The structure of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ also contains other interesting chemical elements:

Magnesium

(Mg)

24 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 - 52;

Binding sites:

The binding sites of Strontium atom in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ (pdb code 4y1j). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 52 binding sites of Strontium where determined in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+, PDB code: 4y1j:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr202 b:59.9 occ:0.58 O A:HOH369 2.6 59.9 1.0 O6 A:G8 2.7 41.9 1.0 O A:HOH349 2.7 53.5 1.0 O A:HOH367 2.8 57.2 1.0 O A:HOH366 2.8 87.5 1.0 O A:HOH368 3.0 57.8 1.0 O A:HOH370 3.1 58.1 1.0 C6 A:G8 3.8 42.0 1.0 SR A:SR212 4.4 96.7 0.7 O5' A:A93 4.5 59.5 1.0 O A:HOH413 4.6 69.5 1.0 C5 A:G8 4.6 36.9 1.0 N7 A:G8 4.6 40.2 1.0 N7 A:G7 4.8 39.9 1.0 OP2 A:G7 4.8 49.3 1.0 N1 A:G8 4.9 44.0 1.0

Strontium binding site 2 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr203 b:60.5 occ:0.69 O6 A:G21 2.5 40.9 1.0 O A:HOH383 2.7 69.2 1.0 O A:HOH334 2.7 36.9 1.0 O A:HOH384 2.8 68.3 1.0 O A:HOH381 2.8 70.3 1.0 O A:HOH333 3.1 48.3 1.0 C6 A:G21 3.6 42.0 1.0 O6 A:G20 3.7 51.4 1.0 SR A:SR209 4.2 55.3 0.8 MG A:MG243 4.4 90.3 1.0 N7 A:G20 4.4 53.3 1.0 C5 A:G21 4.5 42.6 1.0 N1 A:G21 4.6 44.3 1.0 O A:HOH354 4.6 78.0 1.0 O A:HOH385 4.6 80.8 1.0 C6 A:G20 4.6 46.2 1.0 N7 A:G21 4.7 43.1 1.0 MG A:MG245 4.7 73.8 1.0 O A:HOH382 4.8 64.5 1.0 O6 A:G19 4.9 49.9 1.0 C5 A:G20 4.9 47.6 1.0 N7 A:G19 4.9 45.9 1.0

Strontium binding site 3 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr204 b:58.8 occ:0.81 OP1 A:C45 2.4 46.0 1.0 OP2 A:G9 2.4 41.5 1.0 OP1 A:G8 2.4 32.0 1.0 OP1 A:U39 2.4 33.9 1.0 O A:HOH372 2.5 53.4 1.0 OP1 A:A10 2.6 53.6 1.0 P A:G8 3.6 38.1 1.0 P A:G9 3.6 39.8 1.0 P A:C45 3.7 39.1 1.0 P A:A10 3.8 42.4 1.0 P A:U39 3.8 44.2 1.0 O5' A:G8 4.1 39.2 1.0 C3' A:G9 4.1 38.0 1.0 OP2 A:G8 4.2 33.0 1.0 C3' A:G38 4.2 31.5 1.0 C5' A:G8 4.2 42.3 1.0 OP1 A:G9 4.2 40.6 1.0 O5' A:G9 4.2 46.2 1.0 O3' A:U44 4.4 43.8 1.0 OP2 A:A10 4.4 52.1 1.0 C5' A:G38 4.4 31.9 1.0 OP2 A:C45 4.4 39.0 1.0 O A:HOH313 4.4 61.2 1.0 O3' A:G9 4.4 40.5 1.0 O3' A:G38 4.5 40.2 1.0 C4' A:G38 4.5 37.1 1.0 OP1 A:G38 4.6 41.4 1.0 OP2 A:U39 4.7 46.8 1.0 O A:HOH321 4.7 77.2 1.0 O5' A:C45 4.8 39.4 1.0 O A:HOH414 4.8 61.0 1.0 O5' A:U39 4.8 40.3 1.0 O3' A:G7 4.8 32.4 1.0 SR A:SR210 4.9 60.4 1.0 O3' A:G8 4.9 35.5 1.0 C5' A:C45 5.0 43.2 1.0

Strontium binding site 4 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr205 b:0.9 occ:0.52 SR A:SR222 4.1 0.6 0.4 OP2 A:A53 4.3 0.5 1.0

Strontium binding site 5 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr206 b:58.9 occ:0.18 O4 A:U86 2.6 55.8 1.0 O6 A:G85 2.7 52.6 1.0 SR A:SR224 2.9 98.9 0.4 N7 A:G85 2.9 58.1 1.0 SR A:SR211 3.0 0.6 0.8 C6 A:G85 3.2 51.8 1.0 C5 A:G85 3.3 51.8 1.0 C4 A:U86 3.4 56.7 1.0 N6 A:A71 3.7 46.4 1.0 C5 A:U86 3.9 56.8 1.0 O4 A:U84 4.0 57.5 1.0 C8 A:G85 4.1 61.0 1.0 C4 A:U84 4.2 55.5 1.0 C5 A:U84 4.2 56.3 1.0 N3 A:U86 4.5 52.2 1.0 N1 A:G85 4.5 50.9 1.0 C4 A:G85 4.6 55.6 1.0 N3 A:U84 4.9 58.1 1.0 C6 A:A71 4.9 48.0 1.0 C6 A:U84 5.0 60.4 1.0

Strontium binding site 6 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr207 b:0.1 occ:1.00 O2 A:C45 2.8 61.8 1.0 C2 A:C45 3.6 56.9 1.0 O2' A:C45 4.0 49.2 1.0 N3 A:C45 4.1 57.5 1.0 OP1 A:U47 4.2 52.5 1.0 O A:HOH342 4.2 59.3 1.0 OP2 A:U47 4.2 46.5 1.0 N1 A:C45 4.5 48.6 1.0 C5 A:U43 4.5 47.0 1.0 C6 A:U43 4.5 40.2 1.0 C1' A:C45 4.6 43.9 1.0 P A:U47 4.7 53.5 1.0 C2' A:C45 4.9 47.0 1.0

Strontium binding site 7 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr208 b:53.0 occ:0.74 O A:HOH346 2.4 45.8 1.0 O A:HOH355 2.5 53.9 1.0 O A:HOH387 2.6 64.2 1.0 O4 A:U68 2.6 44.9 1.0 O A:HOH397 2.6 80.6 1.0 O A:HOH398 2.7 52.2 1.0 O A:HOH396 3.1 62.5 1.0 C4 A:U68 3.7 47.4 1.0 C5 A:U68 4.3 43.6 1.0 O A:HOH347 4.3 48.6 1.0 N6 A:A30 4.5 45.5 1.0 O6 A:G67 4.6 48.3 1.0 N7 A:G67 4.7 50.0 1.0 O4 A:U69 4.8 52.5 1.0 N3 A:U68 4.8 50.2 1.0 O4 A:U87 4.9 46.0 1.0 O A:HOH401 5.0 51.6 1.0

Strontium binding site 8 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr209 b:55.3 occ:0.77 N7 A:G21 2.5 43.1 1.0 O A:HOH333 2.6 48.3 1.0 O A:HOH354 2.6 78.0 1.0 O A:HOH334 2.7 36.9 1.0 O A:HOH337 2.8 50.5 1.0 C8 A:G21 3.4 41.6 1.0 C5 A:G21 3.4 42.6 1.0 O6 A:G21 3.6 40.9 1.0 C6 A:G21 3.9 42.0 1.0 O A:HOH384 4.2 68.3 1.0 SR A:SR203 4.2 60.5 0.7 N7 A:G20 4.2 53.3 1.0 O A:HOH385 4.3 80.8 1.0 N9 A:G21 4.5 41.7 1.0 C4 A:G21 4.6 45.3 1.0 C8 A:G20 4.6 53.8 1.0 OP2 A:G21 4.6 57.6 1.0 OP2 A:A23 4.7 46.5 1.0 OP2 A:G20 5.0 60.0 1.0 C5 A:G20 5.0 47.6 1.0

Strontium binding site 9 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr210 b:60.4 occ:1.00 OP1 A:G9 2.3 40.6 1.0 OP2 A:C45 2.4 39.0 1.0 O4 A:U41 2.4 41.7 1.0 OP2 A:C40 2.4 35.8 1.0 OP2 A:U39 2.5 46.8 1.0 O A:HOH330 2.6 37.4 1.0 C4 A:U41 3.3 36.5 1.0 P A:G9 3.6 39.8 1.0 P A:U39 3.6 44.2 1.0 P A:C45 3.6 39.1 1.0 C5 A:U41 3.7 40.5 1.0 OP1 A:U39 3.7 33.9 1.0 P A:C40 3.9 42.4 1.0 OP1 A:C45 4.1 46.0 1.0 O5' A:G9 4.1 46.2 1.0 O A:HOH410 4.2 64.5 1.0 O A:HOH356 4.2 60.4 1.0 OP2 A:G9 4.3 41.5 1.0 O A:HOH345 4.3 40.4 1.0 O3' A:U44 4.5 43.8 1.0 N3 A:U41 4.6 41.3 1.0 O3' A:U39 4.6 46.9 1.0 C4' A:U44 4.6 43.6 1.0 O5' A:U39 4.6 40.3 1.0 OP1 A:C40 4.6 42.6 1.0 O3' A:G8 4.7 35.5 1.0 O A:HOH409 4.7 50.5 1.0 C3' A:U39 4.7 44.2 1.0 O5' A:C40 4.7 45.3 1.0 O5' A:C45 4.7 39.4 1.0 O3' A:G38 4.8 40.2 1.0 C5' A:U39 4.8 33.1 1.0 C5 A:C40 4.8 32.8 1.0 O A:HOH389 4.9 51.5 1.0 SR A:SR204 4.9 58.8 0.8 C3' A:U44 5.0 41.1 1.0

Strontium binding site 10 out of 52 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr211 b:0.6 occ:0.82 SR A:SR206 3.0 58.9 0.2 O4 A:U84 3.9 57.5 1.0 C5 A:U84 4.0 56.3 1.0 C4 A:U84 4.3 55.5 1.0 SR A:SR224 4.5 98.9 0.4 SR A:SR215 4.5 0.4 0.7 OP2 A:U84 4.5 81.7 1.0 O6 A:G85 4.5 52.6 1.0 N6 A:A71 4.8 46.4 1.0 OP2 A:A83 4.9 72.0 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