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Magnesium in PDB 5d5l: PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+

Protein crystallography data

The structure of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+, PDB code: 5d5l was solved by J.E.Wedekind, J.A.Liberman, M.Salim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.37 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.358, 57.833, 99.493, 90.00, 107.64, 90.00
R / Rfree (%) 19.9 / 24.7

Other elements in 5d5l:

The structure of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ also contains other interesting chemical elements:

Caesium (Cs) 32 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ (pdb code 5d5l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+, PDB code: 5d5l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 5d5l

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Magnesium binding site 1 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg118

b:0.0
occ:1.00
O A:HOH236 2.1 43.8 1.0
O A:HOH220 2.1 62.0 1.0
O A:HOH202 2.1 72.5 1.0
O A:HOH235 2.1 64.7 1.0
O A:HOH216 2.1 42.7 1.0
OP1 A:U41 2.1 25.9 1.0
P A:U41 3.5 28.4 1.0
H5'' A:U41 3.6 26.8 1.0
HO2' A:U53 3.8 38.3 1.0
O2' A:U53 4.0 31.9 1.0
OP2 A:A24 4.1 29.5 1.0
O5' A:U41 4.1 22.3 1.0
OP1 A:A24 4.1 31.5 1.0
OP1 A:G23 4.2 42.8 1.0
C5' A:U41 4.3 22.3 1.0
OP2 A:A55 4.3 37.0 1.0
OP2 A:U41 4.4 34.3 1.0
P A:A24 4.6 27.2 1.0
O3' A:U40 4.6 33.6 1.0
H5' A:U41 4.6 26.8 1.0
H5' A:U54 4.6 49.4 1.0
H5'' A:G23 4.7 44.0 1.0
H4' A:U53 4.8 43.8 1.0
O A:HOH245 4.9 31.4 1.0

Magnesium binding site 2 out of 15 in 5d5l

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Magnesium binding site 2 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg119

b:62.0
occ:1.00
O A:HOH238 2.1 90.1 1.0
OP1 A:U51 2.2 62.5 1.0
H5'' A:U51 3.2 70.3 1.0
P A:U51 3.4 53.8 1.0
O A:HOH215 3.7 26.9 1.0
O5' A:U51 3.8 56.8 1.0
C5' A:U51 3.9 58.6 1.0
OP2 A:U51 4.1 51.3 1.0
H5' A:U51 4.1 70.3 1.0
H5'' A:U50 4.4 48.0 1.0
H4' A:U50 4.5 48.5 1.0
H3' A:U50 4.6 47.8 1.0
O3' A:U50 4.7 44.0 1.0
C3' A:U50 5.0 39.9 1.0

Magnesium binding site 3 out of 15 in 5d5l

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Magnesium binding site 3 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg120

b:49.8
occ:1.00
OP1 A:U53 2.1 36.4 1.0
O A:HOH208 2.1 37.1 1.0
O A:HOH219 2.1 55.9 1.0
P A:U53 3.5 37.2 1.0
H5'' A:U53 3.6 46.1 1.0
OP2 A:U54 3.8 48.1 1.0
OP1 A:U54 4.1 48.8 1.0
OP2 A:U53 4.3 37.7 1.0
O5' A:U53 4.3 41.3 1.0
P A:U54 4.4 45.6 1.0
O3' A:A52 4.4 61.0 1.0
C5' A:U53 4.4 38.4 1.0
O3' A:U53 4.8 34.7 1.0
H3' A:U53 4.9 43.3 1.0

Magnesium binding site 4 out of 15 in 5d5l

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Magnesium binding site 4 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg121

b:63.8
occ:1.00
O A:HOH213 2.1 49.8 1.0
O A:HOH241 2.1 49.4 1.0
O A:HOH223 2.1 64.3 1.0
N7 A:G73 2.3 25.4 1.0
C8 A:G73 3.2 24.9 1.0
H8 A:G73 3.3 29.9 1.0
C5 A:G73 3.3 25.9 1.0
O6 A:G73 3.6 38.9 1.0
C6 A:G73 3.9 26.8 1.0
OP2 A:G73 4.1 35.3 1.0
O A:HOH217 4.3 55.1 1.0
N7 A:G74 4.4 35.6 1.0
N9 A:G73 4.4 25.0 1.0
C5 A:A72 4.4 24.9 1.0
C4 A:G73 4.5 25.6 1.0
C6 A:A72 4.6 23.7 1.0
O A:HOH249 4.6 36.2 1.0
N7 A:A72 4.6 25.2 1.0
H2' A:A72 4.6 30.6 1.0
H8 A:G74 4.7 40.0 1.0
C4 A:A72 4.8 30.1 1.0
N6 A:A72 4.8 24.5 1.0
C8 A:G74 4.9 33.4 1.0
H62 A:A72 4.9 29.4 1.0
H3' A:A72 4.9 31.0 1.0
N1 A:A72 5.0 33.2 1.0

Magnesium binding site 5 out of 15 in 5d5l

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Magnesium binding site 5 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg122

b:51.4
occ:1.00
OP2 A:U53 2.2 37.7 1.0
OP2 A:A52 2.4 55.8 1.0
H5'' A:A52 3.3 76.9 1.0
P A:U53 3.7 37.2 1.0
P A:A52 3.8 56.6 1.0
OP1 A:G65 4.0 58.8 1.0
H5 A:U53 4.0 38.9 1.0
C5' A:A52 4.1 64.0 1.0
O5' A:A52 4.3 65.2 1.0
CS A:CS106 4.3 65.5 0.8
OP1 A:U53 4.4 36.4 1.0
O5' A:U53 4.5 41.3 1.0
OP1 A:A52 4.6 61.8 1.0
O3' A:A52 4.6 61.0 1.0
H5' A:A52 4.6 76.9 1.0
H3' A:A52 4.7 76.2 1.0
H6 A:U53 4.7 38.8 1.0
C5 A:U53 4.7 32.5 1.0
O A:HOH208 4.9 37.1 1.0
O3' A:U51 4.9 49.7 1.0
C3' A:A52 5.0 63.5 1.0

Magnesium binding site 6 out of 15 in 5d5l

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Magnesium binding site 6 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg123

b:60.5
occ:1.00
O1A A:GTP1 2.3 71.8 1.0
H2' A:U50 3.0 44.5 1.0
OP2 A:U50 3.1 47.5 1.0
H6 A:U50 3.3 51.3 1.0
C6 A:U50 3.7 42.7 1.0
PA A:GTP1 3.7 66.5 1.0
O1B A:GTP1 3.8 68.8 1.0
O5' A:U50 3.8 44.0 1.0
H8 A:GTP1 3.9 63.4 1.0
C2' A:U50 3.9 37.1 1.0
H5 A:U50 3.9 47.5 1.0
C5 A:U50 4.0 39.5 1.0
P A:U50 4.0 45.0 1.0
HO2' A:U50 4.1 52.5 1.0
O A:HOH251 4.2 92.6 1.0
O2' A:U50 4.2 43.7 1.0
O5' A:GTP1 4.3 60.7 1.0
N1 A:U50 4.4 44.6 1.0
O2A A:GTP1 4.6 78.0 1.0
C8 A:GTP1 4.7 52.9 1.0
PB A:GTP1 4.7 72.5 1.0
H3' A:U50 4.7 47.8 1.0
O3A A:GTP1 4.7 94.7 1.0
C1' A:U50 4.7 36.4 1.0
N7 A:GTP1 4.8 58.0 1.0
O3B A:GTP1 4.8 77.8 1.0
OP1 A:U50 4.8 46.5 1.0
H3' A:G49 4.9 46.7 1.0
C3' A:U50 4.9 39.9 1.0

Magnesium binding site 7 out of 15 in 5d5l

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Magnesium binding site 7 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg110

b:75.9
occ:1.00
OP1 B:A10 2.0 56.8 1.0
O B:HOH219 2.1 71.8 1.0
O B:HOH209 2.1 80.7 1.0
O B:HOH216 2.1 94.8 1.0
O B:HOH250 2.1 76.8 1.0
O B:HOH220 2.1 0.2 1.0
P B:A10 3.3 56.3 1.0
H8 B:A10 3.4 55.9 1.0
H5' B:A10 3.8 65.4 1.0
OP2 B:A10 3.8 58.9 1.0
O4' B:A10 4.1 50.6 1.0
O B:HOH252 4.1 54.3 1.0
C8 B:A10 4.1 46.6 1.0
O5' B:A10 4.2 44.8 1.0
O3' B:G9 4.4 44.5 1.0
CS B:CS102 4.4 66.0 0.8
C5' B:A10 4.4 54.5 1.0
N7 B:A10 4.9 47.8 1.0
C4' B:A10 4.9 48.1 1.0
N9 B:A10 5.0 46.0 1.0

Magnesium binding site 8 out of 15 in 5d5l

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Magnesium binding site 8 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg111

b:55.7
occ:1.00
O B:HOH208 2.1 50.6 1.0
O B:HOH214 2.1 0.6 1.0
O B:HOH234 2.1 94.1 1.0
O B:HOH235 2.1 44.1 1.0
N7 B:G73 2.3 44.9 1.0
C8 B:G73 3.2 47.5 1.0
H8 B:G73 3.3 57.0 1.0
C5 B:G73 3.3 41.3 1.0
O6 B:G73 3.7 55.4 1.0
C6 B:G73 3.9 43.6 1.0
O B:HOH213 4.1 0.9 1.0
OP2 B:G73 4.3 40.0 1.0
N9 B:G73 4.4 41.9 1.0
N7 B:G74 4.4 43.8 1.0
C4 B:G73 4.5 41.7 1.0
C5 B:A72 4.5 46.7 1.0
C6 B:A72 4.6 45.8 1.0
H8 B:G74 4.7 51.5 1.0
N7 B:A72 4.7 49.0 1.0
H2' B:A72 4.8 43.2 1.0
C4 B:A72 4.8 44.2 1.0
N6 B:A72 4.9 51.1 1.0
C8 B:G74 4.9 42.9 1.0
H62 B:A72 4.9 61.3 1.0
H3' B:A72 4.9 47.1 1.0
N1 B:A72 5.0 49.6 1.0

Magnesium binding site 9 out of 15 in 5d5l

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Magnesium binding site 9 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg112

b:61.0
occ:1.00
OP1 B:G42 2.2 53.9 1.0
O B:HOH204 3.2 49.4 1.0
H5'' B:G42 3.5 65.9 1.0
P B:G42 3.6 54.3 1.0
OP1 B:C22 3.7 74.1 1.0
OP2 B:A43 4.1 54.0 1.0
H5'' B:C22 4.2 80.7 1.0
O5' B:G42 4.3 54.2 1.0
C5' B:G42 4.3 54.9 1.0
OP2 B:G42 4.5 53.1 1.0
O3' B:U41 4.6 50.9 1.0
H5' B:G42 4.8 65.9 1.0
OP1 B:G23 4.8 59.2 1.0
OP2 B:G23 4.9 59.0 1.0
P B:C22 4.9 79.8 1.0
O5' B:C22 5.0 67.1 1.0
C5' B:C22 5.0 67.2 1.0

Magnesium binding site 10 out of 15 in 5d5l

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Magnesium binding site 10 out of 15 in the PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of PREQ1-II Riboswitch with An Engineered G-U Wobble Pair Bound to Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg105

b:36.5
occ:1.00
O C:HOH222 2.1 26.0 1.0
O C:HOH223 2.1 49.5 1.0
O C:HOH221 2.1 36.7 1.0
OP1 C:A10 2.1 30.6 1.0
P C:A10 3.5 32.9 1.0
H8 C:A10 3.6 28.5 1.0
H5' C:A10 4.0 34.7 1.0
OP2 C:A10 4.2 41.9 1.0
C8 C:A10 4.3 23.7 1.0
CS C:CS102 4.3 56.4 1.0
O4' C:A10 4.3 31.1 1.0
O5' C:A10 4.4 30.6 1.0
O3' C:G9 4.5 23.9 1.0
C5' C:A10 4.7 28.9 1.0
N7 C:A10 5.0 20.8 1.0

Reference:

I.A.Belashov, J.A.Liberman, M.Salim, J.E.Wedekind. Cesium(I) Binding to G-U-Wobble Base Pairs in PREQ1 Riboswitches with Implications For Crystallographic Phasing To Be Published.
Page generated: Mon Dec 14 20:10:11 2020

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