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

Protein crystallography data

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

Other elements in 4y1i:

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

Barium (Ba) 19 atoms
Manganese (Mn) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 25 binding sites of Magnesium where determined in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+, PDB code: 4y1i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 25 in 4y1i

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Magnesium binding site 1 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:

Magnesium binding site 2 out of 25 in 4y1i

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Magnesium binding site 2 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:85.3
occ:1.00
OP1 A:U64 3.5 67.5 1.0
OP2 A:U64 4.1 48.1 1.0
P A:U64 4.1 65.7 1.0
O3' A:C63 4.5 56.9 1.0
OP2 A:A89 4.6 86.6 1.0
OP1 A:A89 4.7 76.1 1.0
OP2 A:U88 4.7 58.1 1.0
OP1 A:C63 4.7 50.6 1.0
C5 A:U88 4.8 76.8 1.0
C6 A:U88 4.9 68.1 1.0
O5' A:U88 4.9 75.3 1.0
C5' A:C63 5.0 44.1 1.0

Magnesium binding site 3 out of 25 in 4y1i

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Magnesium binding site 3 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:0.4
occ:1.00
O A:HOH320 2.1 88.7 1.0
N7 A:A3 3.2 72.9 1.0
OP2 A:A3 3.8 70.1 1.0
C8 A:A3 3.9 66.6 1.0
O2A A:GTP201 4.3 88.3 1.0
N7 A:GTP201 4.4 74.1 1.0
C5 A:A3 4.4 73.0 1.0
N6 A:A3 4.6 80.0 1.0
C5 A:GTP201 4.7 67.8 1.0
C8 A:GTP201 4.8 73.4 1.0
P A:A3 4.9 0.2 1.0
C6 A:A3 5.0 74.6 1.0
C5' A:GTP201 5.0 80.5 1.0

Magnesium binding site 4 out of 25 in 4y1i

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Magnesium binding site 4 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:53.3
occ:1.00
OP2 A:G62 3.5 46.5 1.0
OP2 A:C31 3.7 42.6 1.0
P A:G62 4.6 54.3 1.0
OP1 A:G62 4.6 60.1 1.0
P A:C31 4.7 63.5 1.0
OP1 A:C31 4.7 60.7 1.0

Magnesium binding site 5 out of 25 in 4y1i

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Magnesium binding site 5 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:0.6
occ:1.00
O3' A:G21 1.9 0.4 1.0
C8 A:A22 2.1 0.2 1.0
N7 A:A22 2.2 99.7 1.0
OP1 A:A22 2.3 0.9 1.0
O2' A:G21 2.4 0.8 1.0
P A:A22 2.5 0.7 1.0
C3' A:G21 2.9 0.1 1.0
C2' A:G21 2.9 0.8 1.0
O5' A:A22 3.0 0.8 1.0
N9 A:A22 3.4 95.0 1.0
C5 A:A22 3.5 88.3 1.0
C4' A:G21 3.9 0.6 1.0
OP2 A:A22 3.9 0.9 1.0
C4 A:A22 4.1 88.0 1.0
N7 A:A23 4.1 0.2 1.0
O4' A:A22 4.1 0.0 1.0
C5' A:A22 4.2 0.2 1.0
C1' A:G21 4.3 0.8 1.0
C1' A:A22 4.4 0.4 1.0
C4' A:A22 4.5 0.8 1.0
C3' A:A22 4.6 0.2 1.0
C6 A:A22 4.6 92.4 1.0
C8 A:A23 4.7 97.3 1.0
O4' A:G21 4.7 0.2 1.0
C5 A:A23 4.8 99.0 1.0
N6 A:A22 4.9 91.0 1.0
C5' A:G21 5.0 0.9 1.0

Magnesium binding site 6 out of 25 in 4y1i

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Magnesium binding site 6 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:33.7
occ:1.00
OP1 A:U39 2.0 57.0 1.0
O A:HOH310 2.1 35.6 1.0
OP2 A:G9 2.1 50.8 1.0
OP1 A:G8 2.1 64.5 1.0
OP1 A:C45 2.2 38.7 1.0
OP1 A:A10 2.3 53.0 1.0
P A:G8 3.2 60.0 1.0
P A:G9 3.3 50.7 1.0
P A:U39 3.3 49.4 1.0
P A:A10 3.6 48.3 1.0
O5' A:G8 3.6 42.8 1.0
P A:C45 3.7 55.2 1.0
OP1 A:G9 3.7 43.5 1.0
C5' A:G8 3.8 42.6 1.0
OP2 A:U39 3.8 65.3 1.0
OP2 A:G8 3.9 46.7 1.0
C3' A:G9 4.1 48.3 1.0
OP2 A:A10 4.1 67.1 1.0
O5' A:G9 4.2 56.3 1.0
O5' A:U39 4.3 43.6 1.0
O3' A:G9 4.3 52.0 1.0
O3' A:U44 4.4 46.3 1.0
C3' A:G38 4.4 35.2 1.0
O3' A:G38 4.4 41.4 1.0
C5' A:G38 4.4 44.1 1.0
OP2 A:C45 4.5 40.6 1.0
O3' A:G8 4.5 58.8 1.0
O3' A:G7 4.6 56.2 1.0
C4' A:G38 4.6 45.3 1.0
O5' A:C45 4.6 43.4 1.0
O5' A:A10 4.7 47.7 1.0
C3' A:G8 4.8 47.7 1.0
C4' A:G8 4.8 45.0 1.0
OP1 A:G38 4.9 60.0 1.0
OP2 A:G46 4.9 45.1 1.0
C4' A:G9 5.0 44.0 1.0
C5' A:G9 5.0 54.2 1.0

Magnesium binding site 7 out of 25 in 4y1i

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Magnesium binding site 7 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:59.7
occ:1.00
O4 B:U43 2.2 67.6 1.0
O2' A:C59 2.5 53.7 1.0
C4 B:U43 3.2 60.9 1.0
O4' A:C60 3.3 55.5 1.0
C2' A:C59 3.5 55.2 1.0
N3 B:U43 3.5 58.9 1.0
N2 B:G94 3.7 61.0 1.0
O2 A:C59 3.8 57.4 1.0
N3 B:A95 3.8 58.4 1.0
C1' A:C59 4.0 54.6 1.0
C1' A:C60 4.2 52.4 1.0
C4' A:C60 4.3 55.6 1.0
O2' B:A95 4.3 67.6 1.0
C2 B:A95 4.4 56.0 1.0
C5' A:C60 4.5 53.5 1.0
N2 A:G46 4.5 61.6 1.0
C5 B:U43 4.6 67.0 1.0
C2 B:G94 4.7 60.9 1.0
C2 A:C59 4.7 64.2 1.0
C3' A:C59 4.8 58.0 1.0
N1 A:C60 4.8 49.4 1.0
C1' B:A95 4.8 60.7 1.0
C2 B:U43 4.8 80.8 1.0
C6 A:C60 4.9 48.4 1.0
N1 A:C59 4.9 60.5 1.0
C4 B:A95 4.9 53.5 1.0
N1 B:G94 4.9 57.6 1.0
C2' B:A95 5.0 63.2 1.0

Magnesium binding site 8 out of 25 in 4y1i

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Magnesium binding site 8 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:92.8
occ:1.00
O2 A:C45 3.3 73.0 1.0
N3 A:C45 3.5 40.9 1.0
C2 A:C45 3.8 50.8 1.0
O A:HOH302 4.4 64.0 1.0
O4 A:U44 4.5 57.6 1.0
C4 A:C45 4.6 35.8 1.0
N4 A:C45 4.9 51.1 1.0

Magnesium binding site 9 out of 25 in 4y1i

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Magnesium binding site 9 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:69.6
occ:1.00
O4 A:U68 2.3 76.8 1.0
C4 A:U68 3.4 51.8 1.0
C5 A:U68 4.0 55.8 1.0
O6 A:G67 4.0 60.6 1.0
N6 A:A30 4.1 56.6 1.0
O4 A:U69 4.4 69.1 1.0
N7 A:G67 4.5 52.5 1.0
N3 A:U68 4.6 55.0 1.0
C6 A:G67 4.6 57.3 1.0
O4 A:U87 4.7 78.5 1.0
C5 A:G67 4.8 51.7 1.0

Magnesium binding site 10 out of 25 in 4y1i

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Magnesium binding site 10 out of 25 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to 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 Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:90.3
occ:1.00
O4 A:U100 3.0 91.5 1.0
C4 A:U100 4.0 83.4 1.0
O4 A:U99 4.2 69.4 1.0
C5 A:U100 4.3 81.3 1.0
C4 A:U99 4.7 72.2 1.0
C5 A:U99 4.8 71.3 1.0

Reference:

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
Page generated: Mon Dec 14 19:48:56 2020

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