Magnesium 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:

Strontium

(Sr)

52 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch A41U Binding Site Mutant in Presence of MN2+, PDB code: 4y1j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 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 Magnesium with other atoms in the Mg 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:Mg232 b:0.5 occ:1.00 OP1 A:G19 2.6 56.1 1.0 OP2 A:G19 3.4 51.9 1.0 P A:G19 3.4 56.1 1.0 OP2 A:G20 4.2 60.0 1.0 O A:HOH385 4.2 80.8 1.0 O5' A:G19 4.2 48.4 1.0 O A:HOH354 4.4 78.0 1.0 O3' A:C18 4.8 55.5 1.0 C5' A:G19 5.0 48.6 1.0

Magnesium binding site 2 out of 24 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 Magnesium with other atoms in the Mg 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:Mg233 b:0.4 occ:1.00 OP1 A:U69 3.3 61.0 1.0 OP1 A:U82 3.3 80.4 1.0 OP2 A:G70 3.7 54.3 1.0 MG A:MG237 3.9 84.8 1.0 OP1 A:G70 3.9 52.1 1.0 P A:G70 4.2 51.1 1.0 O5' A:U69 4.4 46.7 1.0 P A:U69 4.4 60.8 1.0 C5' A:U69 4.4 42.7 1.0 P A:U82 4.4 74.3 1.0 OP2 A:U82 4.6 70.9 1.0 O3' A:U69 4.6 47.8 1.0 SR A:SR215 4.6 0.4 0.7

Magnesium binding site 3 out of 24 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 Magnesium with other atoms in the Mg 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:Mg234 b:90.4 occ:1.00 OP2 A:A95 2.8 49.1 1.0 OP1 A:G94 3.2 50.7 1.0 C5' A:G94 3.4 50.5 1.0 O A:HOH365 3.6 61.9 1.0 P A:A95 3.8 51.3 1.0 P A:G94 3.8 54.4 1.0 O5' A:G94 3.9 51.6 1.0 OP1 A:A95 3.9 49.9 1.0 OP2 A:G94 4.0 52.6 1.0 N4 A:C96 4.1 42.3 1.0 O3' A:G94 4.4 57.4 1.0 C4' A:G94 4.5 47.5 1.0 C3' A:G94 4.7 47.7 1.0

Magnesium binding site 4 out of 24 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 Magnesium with other atoms in the Mg 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:Mg235 b:90.4 occ:1.00 O2' A:A93 2.9 49.9 1.0 O3' A:A93 3.3 61.4 1.0 OP1 A:G94 3.6 50.7 1.0 O5' A:G94 3.9 51.6 1.0 P A:G94 3.9 54.4 1.0 C2' A:A93 4.0 43.2 1.0 C3' A:A93 4.1 44.0 1.0 C4' A:A93 4.4 44.5 1.0

Magnesium binding site 5 out of 24 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 Magnesium with other atoms in the Mg 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:Mg236 b:64.3 occ:1.00 OP2 A:A10 3.3 52.1 1.0 O4' A:G11 3.3 35.8 1.0 O5' A:A10 3.4 57.9 1.0 O3' A:G9 3.6 40.5 1.0 P A:A10 3.8 42.4 1.0 O5' A:G11 3.9 51.7 1.0 C4' A:G11 4.0 41.1 1.0 O A:HOH371 4.2 52.4 1.0 C5' A:G11 4.3 43.6 1.0 O A:HOH413 4.4 69.5 1.0 C5' A:A10 4.5 44.7 1.0 O2' A:G9 4.5 33.2 1.0 C1' A:G11 4.5 42.7 1.0 O3' A:A10 4.8 42.6 1.0 C1' A:G9 4.8 38.5 1.0 O A:HOH414 4.8 61.0 1.0 N9 A:G11 4.8 46.0 1.0 C3' A:G9 4.9 38.0 1.0

Magnesium binding site 6 out of 24 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 Magnesium with other atoms in the Mg 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:Mg237 b:84.8 occ:1.00 OP1 A:U69 2.8 61.0 1.0 O3' A:U68 3.4 51.9 1.0 C5' A:U69 3.4 42.7 1.0 P A:U69 3.6 60.8 1.0 MG A:MG233 3.9 0.4 1.0 O5' A:U69 4.0 46.7 1.0 O2' A:U68 4.6 51.6 1.0 C3' A:U68 4.7 50.7 1.0 C4' A:U69 4.8 42.1 1.0

Magnesium binding site 7 out of 24 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 Magnesium with other atoms in the Mg 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:Mg238 b:0.9 occ:1.00 SR A:SR222 3.0 0.6 0.4 OP2 A:G48 3.4 71.8 1.0 N7 A:G48 3.9 47.3 1.0 C8 A:G48 4.0 45.7 1.0 O A:HOH394 4.0 80.3 1.0 OP2 A:U47 4.2 46.5 1.0 O A:HOH415 4.3 82.8 1.0 C5' A:G48 4.7 63.4 1.0 P A:G48 4.8 70.4 1.0 C5 A:U47 4.9 39.8 1.0 O5' A:U47 4.9 53.0 1.0

Magnesium binding site 8 out of 24 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 Magnesium with other atoms in the Mg 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:Mg239 b:0.1 occ:1.00 O2 A:C91 3.3 39.4 1.0 O2' A:C91 3.7 50.6 1.0 N2 A:G14 3.8 38.8 1.0 C2' A:C91 4.4 43.4 1.0 C2 A:C91 4.5 43.0 1.0 O4' A:A92 4.5 46.1 1.0 C1' A:C91 4.7 40.3 1.0 C1' A:A92 4.9 44.9 1.0

Magnesium binding site 9 out of 24 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 Magnesium with other atoms in the Mg 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:Mg240 b:98.9 occ:1.00 O A:HOH375 2.6 80.9 1.0 OP2 A:C91 3.2 43.6 1.0 OP1 A:C91 3.5 53.6 1.0 SR A:SR223 3.8 0.3 0.6 P A:C91 3.9 49.7 1.0 MG A:MG241 4.9 77.2 1.0 O5' A:C91 5.0 41.1 1.0

Magnesium binding site 10 out of 24 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 Magnesium with other atoms in the Mg 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:Mg241 b:77.2 occ:1.00 OP1 A:C91 2.8 53.6 1.0 O3' A:G90 3.3 42.4 1.0 P A:C91 3.6 49.7 1.0 O A:HOH314 3.9 76.0 1.0 C3' A:G90 4.5 41.7 1.0 OP2 A:C91 4.6 43.6 1.0 C5' A:G90 4.7 47.3 1.0 C4' A:G90 4.7 50.9 1.0 O5' A:C91 4.9 41.1 1.0 MG A:MG240 4.9 98.9 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