Barium in PDB 4y1i: Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+

The structure of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+, PDB code: 4y1i 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)	55.90 / 2.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.285, 127.881, 115.324, 90.00, 93.37, 90.00
R / Rfree (%)	19.3 / 22.4

The structure of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ also contains other interesting chemical elements:

Magnesium	(Mg)	25 atoms
Manganese	(Mn)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Barium atom in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ (pdb code 4y1i). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 19 binding sites of Barium where determined in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+, PDB code: 4y1i:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba213 b:69.8 occ:1.00 O4 A:U36 2.7 53.1 1.0 O6 A:G62 2.8 55.7 1.0 O6 A:G35 2.8 46.1 1.0 O A:HOH304 3.1 50.5 1.0 O6 A:G61 3.2 57.1 1.0 C4 A:U36 3.7 40.2 1.0 C6 A:G35 3.9 42.2 1.0 C6 A:G62 3.9 46.9 1.0 C6 A:G61 4.0 53.5 1.0 N3 A:U36 4.1 35.3 1.0 N4 A:C63 4.2 50.4 1.0 N4 A:C37 4.3 38.5 1.0 N7 A:G35 4.5 43.5 1.0 N7 A:G62 4.5 47.5 1.0 C5 A:G35 4.6 42.2 1.0 C5 A:G62 4.6 43.2 1.0 N1 A:G61 4.7 54.4 1.0 C5 A:G61 4.8 51.8 1.0 N1 A:G35 4.9 32.1 1.0

Barium binding site 2 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba214 b:0.6 occ:1.00 O A:HOH309 3.0 64.8 1.0 O6 A:G6 3.2 63.6 1.0 N7 A:G6 3.7 68.8 1.0 C6 A:G6 4.0 57.2 1.0 N7 A:A5 4.1 69.6 1.0 C5 A:G6 4.2 57.3 1.0 O6 A:G7 4.2 64.3 1.0 N6 A:A5 4.5 63.6 1.0 OP1 A:G94 4.7 73.4 1.0 C5 A:A5 4.7 55.2 1.0 C8 A:A5 4.9 67.8 1.0 BA A:BA220 4.9 0.5 1.0 C8 A:G6 4.9 65.8 1.0 C6 A:A5 4.9 61.7 1.0

Barium binding site 3 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba215 b:0.6 occ:1.00 N7 A:G51 3.4 82.5 1.0 O6 A:G51 3.9 88.2 1.0 C5 A:G51 4.2 71.4 1.0 C8 A:G51 4.3 82.8 1.0 C6 A:G51 4.4 76.4 1.0 N7 A:G50 4.5 64.2 1.0 OP2 A:G50 5.0 72.9 1.0 O A:HOH312 5.0 63.8 1.0 C8 A:G50 5.0 70.8 1.0

Barium binding site 4 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba216 b:0.0 occ:1.00 O A:HOH308 3.2 0.1 1.0 N7 A:G21 3.4 0.7 1.0 O6 A:G21 3.7 0.5 1.0 C5 A:G21 3.9 0.2 1.0 C6 A:G21 4.0 0.5 1.0 OP1 A:A23 4.1 0.9 1.0 C8 A:G21 4.3 0.9 1.0 C4 A:G21 4.9 0.1 1.0

Barium binding site 5 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba217 b:0.2 occ:1.00 O A:HOH321 2.7 0.5 1.0 O6 A:G21 2.8 0.5 1.0 O A:HOH311 3.6 89.4 1.0 O A:HOH308 3.7 0.1 1.0 C6 A:G21 3.9 0.5 1.0 O6 A:G20 4.1 0.0 1.0 N1 A:G21 4.6 0.6 1.0 O A:HOH306 4.6 77.8 1.0 O6 A:G19 4.9 0.3 1.0

Barium binding site 6 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba218 b:0.9 occ:1.00 OP1 A:A79 3.4 74.0 1.0 OP2 A:A79 3.9 70.2 1.0 O6 A:G77 4.0 85.3 1.0 N7 A:G77 4.0 59.1 1.0 P A:A79 4.1 68.8 1.0 C6 A:G77 4.2 65.9 1.0 C5 A:G77 4.2 54.5 1.0 O3' A:A78 4.8 76.9 1.0 C8 A:G77 4.8 57.9 1.0

Barium binding site 7 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba219 b:0.5 occ:1.00 O6 A:G85 4.2 60.0 1.0 N7 A:G85 4.6 35.4 1.0 O4 A:U84 4.7 48.1 1.0 C5 A:U84 4.9 46.4 1.0 OP2 A:U69 5.0 63.1 1.0

Barium binding site 8 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba220 b:0.5 occ:1.00 O6 A:G8 3.2 71.0 1.0 O A:HOH309 4.1 64.8 1.0 C6 A:G8 4.2 66.4 1.0 N7 A:G7 4.4 49.3 1.0 OP2 A:G7 4.4 53.2 1.0 OP2 A:G6 4.5 59.1 1.0 N7 A:G8 4.6 62.5 1.0 N7 A:G6 4.8 68.8 1.0 C5 A:G8 4.8 61.9 1.0 BA A:BA214 4.9 0.6 1.0

Barium binding site 9 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba221 b:0.8 occ:1.00 O2 A:C40 2.8 75.2 1.0 O4 A:U39 3.5 71.0 1.0 C2 A:C40 3.8 48.1 1.0 C4 A:U39 4.3 52.4 1.0 N3 A:C40 4.4 56.7 1.0 N3 A:U39 4.5 55.9 1.0 N1 A:C40 4.8 41.6 1.0 C1' A:C40 4.8 62.3 1.0

Barium binding site 10 out of 19 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba222 b:0.9 occ:1.00 OP2 A:A13 3.2 76.3 1.0 O2' A:G11 3.7 68.2 1.0 O6 A:G14 3.8 79.2 1.0 OP2 A:U12 3.9 53.2 1.0 N1 A:A92 4.3 77.5 1.0 O3' A:G11 4.4 43.8 1.0 C2 A:A92 4.4 79.6 1.0 N7 A:G14 4.7 81.2 1.0 P A:A13 4.7 65.6 1.0 P A:U12 4.7 52.2 1.0 C6 A:G14 4.8 76.4 1.0 C2' A:G11 4.9 61.7 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