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Magnesium in PDB 2cky: Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand

Protein crystallography data

The structure of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand, PDB code: 2cky was solved by S.Thore, M.Leibundgut, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.9
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.850, 98.670, 54.550, 90.00, 104.80, 90.00
R / Rfree (%) 18.3 / 25

Other elements in 2cky:

The structure of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand also contains other interesting chemical elements:

Osmium (Os) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand (pdb code 2cky). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand, PDB code: 2cky:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2cky

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Magnesium binding site 1 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1078

b:55.5
occ:1.00
 MG A:MG1080 2.6 18.4 1.0
O6 A:G71 3.1 41.2 1.0
OP2 A:G69 3.9 69.0 1.0
C6 A:G71 4.3 40.8 1.0
N7 A:G70 4.4 46.3 1.0
O6 A:G42 4.9 51.5 1.0
OP2 A:G70 4.9 65.9 1.0

Magnesium binding site 2 out of 10 in 2cky

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Magnesium binding site 2 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1079

b:19.5
occ:1.00
 N7 A:A29 2.5 32.8 1.0
C8 A:A29 3.5 33.3 1.0
C5 A:A29 3.5 32.2 1.0
N6 A:A29 3.7 31.8 1.0
OP2 A:A44 3.9 28.9 1.0
C6 A:A29 4.0 32.0 1.0
O2' A:G28 4.4 35.5 1.0
O6 A:G30 4.6 28.0 1.0
N9 A:A29 4.7 33.2 1.0
C4 A:A29 4.7 32.7 1.0

Magnesium binding site 3 out of 10 in 2cky

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Magnesium binding site 3 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1080

b:18.4
occ:1.00
 MG A:MG1078 2.6 55.5 1.0
O6 A:G71 3.8 41.2 1.0
O6 A:G70 4.0 42.6 1.0
O6 A:G69 4.3 56.5 1.0
N7 A:G69 4.3 59.9 1.0
OP2 A:G69 4.5 69.0 1.0
OP2 A:A43 4.5 40.2 1.0
N7 A:G70 4.6 46.3 1.0
C6 A:G71 4.6 40.8 1.0
N6 A:A43 4.7 41.2 1.0
C6 A:A43 4.8 40.5 1.0
C6 A:G69 4.9 58.3 1.0
N1 A:G71 4.9 39.4 1.0
C6 A:G70 4.9 43.5 1.0
C5 A:A43 5.0 39.9 1.0
C5 A:G69 5.0 59.6 1.0

Magnesium binding site 4 out of 10 in 2cky

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Magnesium binding site 4 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1081

b:40.1
occ:1.00
 OP2 A:A4 2.7 51.2 1.0
OP1 A:A4 3.0 51.8 1.0
OP1 A:G3 3.1 50.1 1.0
P A:A4 3.2 53.5 1.0
O3' A:G3 3.7 52.9 1.0
P A:G3 4.1 52.7 1.0
O5' A:G3 4.1 53.7 1.0
C5' A:G3 4.2 52.6 1.0
C3' A:G3 4.2 53.0 1.0
O5' A:A4 4.7 53.8 1.0
C4' A:G3 4.7 53.3 1.0
OP2 A:G3 4.8 50.9 1.0

Magnesium binding site 5 out of 10 in 2cky

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Magnesium binding site 5 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1082

b:19.9
occ:1.00
 O6 A:G66 2.3 56.4 1.0
O6 A:G48 2.6 61.4 1.0
O2B A:TPP1084 3.0 46.6 1.0
O1A A:TPP1084 3.0 37.8 1.0
O2A A:TPP1084 3.1 38.5 1.0
C6 A:G66 3.3 56.0 1.0
PA A:TPP1084 3.5 39.0 1.0
N4 A:C65 3.6 50.4 1.0
N1 A:G66 3.6 54.7 1.0
C6 A:G48 3.8 62.4 1.0
O3A A:TPP1084 4.0 43.3 1.0
N3 A:C65 4.0 52.6 1.0
PB A:TPP1084 4.1 49.1 1.0
O4 A:U47 4.1 51.1 1.0
C4 A:C65 4.3 51.5 1.0
N1 A:G48 4.4 62.9 1.0
N1 A:A49 4.6 65.8 1.0
C5 A:G66 4.6 56.9 1.0
O6 A:G64 4.7 53.0 1.0
C2 A:A49 4.8 65.3 1.0
O3B A:TPP1084 4.9 46.6 1.0
C2 A:G66 5.0 54.5 1.0

Magnesium binding site 6 out of 10 in 2cky

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Magnesium binding site 6 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1078

b:31.4
occ:1.00
 N7 B:A29 2.4 23.4 1.0
C8 B:A29 3.1 24.2 1.0
C5 B:A29 3.7 23.6 1.0
N6 B:A29 4.2 26.2 1.0
OP2 B:A44 4.2 35.3 1.0
C6 B:A29 4.4 25.1 1.0
O6 B:G30 4.4 26.6 1.0
N9 B:A29 4.4 25.2 1.0
O2' B:G28 4.6 36.8 1.0
C4 B:A29 4.7 24.9 1.0

Magnesium binding site 7 out of 10 in 2cky

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Magnesium binding site 7 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1079

b:92.1
occ:1.00
 OP2 B:G70 2.7 83.1 1.0
O6 B:G42 3.4 64.2 1.0
P B:G70 3.6 87.5 1.0
O5' B:G70 3.6 82.8 1.0
OP1 B:G70 4.1 92.9 1.0
C6 B:G42 4.2 62.9 1.0
O6 B:G71 4.4 54.7 1.0
N7 B:G71 4.5 59.2 1.0
OP2 B:G71 4.6 74.4 1.0
C8 B:G70 4.7 65.4 1.0
N1 B:G42 4.7 63.5 1.0
C5' B:G70 4.9 84.4 1.0
C3' B:G70 5.0 76.5 1.0
O3' B:G69 5.0 89.5 1.0

Magnesium binding site 8 out of 10 in 2cky

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Magnesium binding site 8 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1080

b:26.2
occ:1.00
 O6 B:G66 2.0 57.4 1.0
O6 B:G48 2.1 60.1 1.0
O1A B:TPP1082 2.3 44.7 1.0
N1 B:A49 3.1 68.1 1.0
C6 B:G48 3.1 61.2 1.0
C6 B:G66 3.1 57.0 1.0
N1 B:G48 3.4 61.3 1.0
C2 B:A49 3.6 67.9 1.0
PA B:TPP1082 3.6 42.6 1.0
N1 B:G66 3.7 55.3 1.0
N3 B:C65 3.7 54.7 1.0
O4 B:U47 3.7 52.4 1.0
O2A B:TPP1082 3.7 32.0 1.0
C6 B:A49 4.1 68.5 1.0
O2B B:TPP1082 4.2 47.4 1.0
C5 B:G66 4.3 58.4 1.0
O2 B:C65 4.3 60.7 1.0
N6 B:A49 4.4 69.0 1.0
C5 B:G48 4.4 62.7 1.0
O6 B:G64 4.4 53.0 1.0
O3A B:TPP1082 4.4 44.2 1.0
N4 B:C65 4.4 51.1 1.0
C2 B:C65 4.5 58.2 1.0
C4 B:C65 4.6 52.6 1.0
C4 B:U47 4.7 53.2 1.0
C2 B:G48 4.8 62.9 1.0
O7 B:TPP1082 4.8 38.2 1.0
N3 B:A49 4.9 69.0 1.0
N7 B:G66 4.9 62.1 1.0
N6 B:A68 5.0 71.9 1.0

Magnesium binding site 9 out of 10 in 2cky

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Magnesium binding site 9 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1083

b:81.1
occ:1.00
 OP2 B:U12 3.8 37.0 1.0
O5' B:G11 4.5 38.4 1.0
C5' B:G11 4.5 38.2 1.0
OP1 B:G11 4.6 37.4 1.0
P B:U12 4.9 36.2 1.0
O3' B:C46 4.9 51.2 1.0
OP1 B:U47 5.0 54.5 1.0

Magnesium binding site 10 out of 10 in 2cky

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Magnesium binding site 10 out of 10 in the Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Arabidopsis Thaliana Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1084

b:92.9
occ:1.00
 O2' B:U19 3.8 44.9 1.0
O4 B:U15 4.1 27.0 1.0
O6 B:G17 4.6 33.3 1.0
O4 B:U16 4.6 37.0 1.0
O3' B:U19 4.7 48.0 1.0
C4 B:U15 4.8 24.6 1.0
C2' B:U19 4.9 46.0 1.0
N4 B:C22 5.0 33.3 1.0

Reference:

S.Thore, M.Leibundgut, N.Ban. Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand. Science V. 312 1208 2006.
ISSN: ISSN 0036-8075
PubMed: 16675665
DOI: 10.1126/SCIENCE.1128451
Page generated: Mon Dec 14 07:19:17 2020

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