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Magnesium in PDB 3d2g: Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch

Protein crystallography data

The structure of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch, PDB code: 3d2g was solved by S.Thore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.048, 111.022, 55.733, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch (pdb code 3d2g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch, PDB code: 3d2g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3d2g

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Magnesium binding site 1 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg78

b:47.0
occ:1.00
 O2B B:TPP83 2.0 43.6 1.0
O B:HOH86 2.1 47.5 1.0
O B:HOH84 2.2 42.5 1.0
O B:HOH85 2.2 47.3 1.0
O6 B:G48 2.4 37.0 1.0
O6 B:G66 2.5 41.5 1.0
PB B:TPP83 3.2 47.0 1.0
C6 B:G66 3.3 34.5 1.0
N1 B:G66 3.4 35.1 1.0
C6 B:G48 3.5 36.4 1.0
O B:HOH93 3.6 38.0 1.0
O1B B:TPP83 3.6 39.7 1.0
O3A B:TPP83 3.7 61.7 1.0
N1 B:G48 3.9 33.4 1.0
O4 B:U47 4.1 38.7 1.0
N1 B:A49 4.2 36.1 1.0
N3 B:C65 4.2 31.6 1.0
O3B B:TPP83 4.3 51.1 1.0
O B:HOH98 4.3 51.0 1.0
N4 B:C65 4.4 34.4 1.0
C2 B:A49 4.4 35.4 1.0
O1A B:TPP83 4.4 62.8 1.0
PA B:TPP83 4.5 56.8 1.0
C5 B:G66 4.7 36.4 1.0
C5 B:G48 4.8 36.6 1.0
C2 B:G66 4.8 35.0 1.0
O2A B:TPP83 4.8 55.1 1.0
C4 B:C65 4.8 37.6 1.0

Magnesium binding site 2 out of 10 in 3d2g

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Magnesium binding site 2 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg79

b:58.0
occ:1.00
 O B:HOH88 2.1 46.5 1.0
O A:HOH84 2.1 62.9 1.0
O B:HOH87 2.2 65.3 1.0
O B:HOH89 2.2 52.3 1.0
OP1 B:C51 2.2 34.2 1.0
OP2 B:A52 2.6 37.4 1.0
P B:C51 3.4 36.0 1.0
OP2 B:C51 3.6 28.7 1.0
O B:HOH123 3.7 47.6 1.0
N1 A:A50 3.8 39.2 1.0
P B:A52 4.1 44.2 1.0
C2 A:A50 4.2 35.8 1.0
O B:HOH108 4.5 66.7 1.0
O3' B:A50 4.5 32.5 1.0
O5' B:C51 4.5 32.9 1.0
C3' B:C51 4.7 38.7 1.0
O3' B:C51 4.8 39.7 1.0
C6 A:A50 4.8 39.4 1.0
N7 B:A52 4.9 44.6 1.0
O5' B:A52 4.9 42.5 1.0
OP1 B:A52 5.0 38.9 1.0

Magnesium binding site 3 out of 10 in 3d2g

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Magnesium binding site 3 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg78

b:47.3
occ:1.00
 O1A A:TPP83 1.9 43.5 1.0
O A:HOH89 2.2 44.2 1.0
O A:HOH92 2.2 57.7 1.0
O A:HOH91 2.2 44.6 1.0
O A:HOH90 2.2 44.0 1.0
O3B A:TPP83 2.4 42.7 1.0
PA A:TPP83 3.2 56.2 1.0
O A:HOH115 3.3 52.5 1.0
PB A:TPP83 3.5 42.7 1.0
O3A A:TPP83 3.8 50.4 1.0
O2B A:TPP83 3.8 44.6 1.0
O A:HOH106 3.8 56.0 1.0
O4 A:U63 4.1 33.1 1.0
O A:HOH161 4.1 59.9 1.0
O2A A:TPP83 4.1 59.0 1.0
O6 A:G64 4.2 28.7 1.0
O7 A:TPP83 4.2 61.9 1.0
N4 A:C65 4.4 24.6 1.0
O A:HOH142 4.4 65.1 1.0
O A:HOH119 4.5 55.0 1.0
O2' A:G60 4.7 50.9 1.0
C4 A:U63 4.7 36.0 1.0
O A:HOH162 4.7 59.0 1.0
C5 A:U63 4.8 33.9 1.0
O A:HOH95 4.8 44.9 1.0
O1B A:TPP83 4.8 47.2 1.0
N7 A:G64 4.9 30.9 1.0
O A:HOH93 4.9 50.3 1.0

Magnesium binding site 4 out of 10 in 3d2g

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Magnesium binding site 4 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg79

b:49.7
occ:1.00
 O2B A:TPP83 2.0 44.6 1.0
O A:HOH94 2.1 40.8 1.0
O A:HOH93 2.1 50.3 1.0
O A:HOH95 2.2 44.9 1.0
O6 A:G48 2.3 28.7 1.0
O6 A:G66 2.6 30.6 1.0
PB A:TPP83 3.3 42.7 1.0
C6 A:G66 3.4 30.1 1.0
C6 A:G48 3.4 28.6 1.0
N1 A:G66 3.7 27.4 1.0
O A:HOH91 3.9 44.6 1.0
O3A A:TPP83 3.9 50.4 1.0
N1 A:G48 3.9 23.4 1.0
O4 A:U47 4.0 28.6 1.0
N1 A:A49 4.1 30.8 1.0
O1B A:TPP83 4.1 47.2 1.0
O3B A:TPP83 4.2 42.7 1.0
O2A A:TPP83 4.2 59.0 1.0
C2 A:A49 4.2 26.7 1.0
O A:HOH103 4.4 56.2 1.0
N3 A:C65 4.5 24.5 1.0
PA A:TPP83 4.6 56.2 1.0
N4 A:C65 4.6 24.6 1.0
C5 A:G48 4.7 24.1 1.0
O A:HOH111 4.7 55.4 1.0
O A:HOH161 4.7 59.9 1.0
C5 A:G66 4.8 29.6 1.0
O1A A:TPP83 4.8 43.5 1.0
C4 A:U47 4.8 30.1 1.0

Magnesium binding site 5 out of 10 in 3d2g

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Magnesium binding site 5 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg80

b:64.9
occ:1.00
 O B:HOH90 2.1 54.7 1.0
O A:HOH98 2.1 50.7 1.0
O A:HOH97 2.2 52.5 1.0
O A:HOH96 2.2 41.2 1.0
OP2 A:A52 2.4 35.0 1.0
OP1 A:C51 2.4 38.7 1.0
P A:C51 3.6 39.3 1.0
O A:HOH153 3.8 51.1 1.0
P A:A52 3.9 46.8 1.0
OP2 A:C51 3.9 40.1 1.0
N1 B:A50 4.1 32.7 1.0
O A:HOH152 4.2 56.0 1.0
O A:HOH124 4.3 50.7 1.0
C2 B:A50 4.4 31.6 1.0
O5' A:A52 4.5 47.8 1.0
N7 A:A52 4.6 35.5 1.0
O A:HOH177 4.7 51.5 1.0
O5' A:C51 4.7 42.1 1.0
O3' A:A50 4.7 35.4 1.0
C8 A:A52 4.8 35.5 1.0
C3' A:C51 4.8 43.0 1.0
O3' A:C51 4.9 42.5 1.0
OP1 A:A52 4.9 40.5 1.0

Magnesium binding site 6 out of 10 in 3d2g

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Magnesium binding site 6 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg80

b:50.1
occ:1.00
 O B:HOH91 2.1 43.3 1.0
O B:HOH92 2.2 46.4 1.0
O B:HOH93 2.2 38.0 1.0
O B:HOH94 2.2 46.6 1.0
O2A B:TPP83 2.3 55.1 1.0
O3B B:TPP83 2.5 51.1 1.0
O4 B:U63 3.5 41.2 1.0
PB B:TPP83 3.7 47.0 1.0
PA B:TPP83 3.7 56.8 1.0
O2B B:TPP83 3.8 43.6 1.0
C5 B:U63 3.9 45.3 1.0
O6 B:G64 4.0 33.5 1.0
C4 B:U63 4.0 42.7 1.0
N4 B:C65 4.0 34.4 1.0
N7 B:G64 4.1 35.4 1.0
O3A B:TPP83 4.2 61.7 1.0
O B:HOH112 4.4 47.3 1.0
O B:HOH103 4.5 71.2 1.0
O2' B:G60 4.6 89.2 1.0
O7 B:TPP83 4.6 58.7 1.0
O1A B:TPP83 4.8 62.8 1.0
C6 B:G64 4.8 38.8 1.0
C5 B:G64 4.8 40.9 1.0
C4 B:C65 4.9 37.6 1.0
O1B B:TPP83 5.0 39.7 1.0
C6 B:U63 5.0 45.5 1.0

Magnesium binding site 7 out of 10 in 3d2g

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Magnesium binding site 7 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg82

b:81.1
occ:1.00
 O A:HOH85 2.2 54.9 1.0
O A:HOH87 2.2 52.3 1.0
O A:HOH88 2.2 52.5 1.0
O A:HOH86 2.2 68.9 1.0
OP2 A:G42 2.6 35.6 1.0
P A:G42 3.8 41.9 1.0
OP1 A:G42 4.2 42.3 1.0
O A:HOH128 4.3 54.5 1.0
C5' A:U41 4.5 45.5 1.0
C4' A:U41 4.6 42.8 1.0
O3' A:U41 4.8 49.0 1.0
O5' A:G42 4.9 36.3 1.0

Magnesium binding site 8 out of 10 in 3d2g

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Magnesium binding site 8 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg81

b:61.7
occ:1.00
 O A:HOH101 2.2 50.8 1.0
O A:HOH100 2.2 52.7 1.0
O A:HOH99 2.2 53.9 1.0
O A:HOH132 2.4 64.2 1.0
O A:HOH158 2.6 68.1 1.0
N7 A:A29 2.9 41.2 1.0
C8 A:A29 3.7 44.0 1.0
OP2 A:A44 4.0 41.2 1.0
C5 A:A29 4.0 43.2 1.0
N6 A:A29 4.2 35.3 1.0
C6 A:A29 4.6 41.1 1.0
O A:HOH172 4.7 66.5 1.0
O6 A:G30 4.8 37.3 1.0

Magnesium binding site 9 out of 10 in 3d2g

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Magnesium binding site 9 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg81

b:63.6
occ:1.00
 N7 B:A29 2.5 51.8 1.0
O B:HOH102 2.5 44.3 1.0
O B:HOH104 2.6 66.8 1.0
C8 B:A29 3.4 55.2 1.0
C5 B:A29 3.6 54.6 1.0
N6 B:A29 3.7 48.1 1.0
C6 B:A29 4.1 51.5 1.0
O2' B:G28 4.2 54.3 1.0
O6 B:G30 4.6 45.2 1.0
N9 B:A29 4.6 56.3 1.0
C4 B:A29 4.7 56.4 1.0
OP2 B:A44 4.7 38.6 1.0

Magnesium binding site 10 out of 10 in 3d2g

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Magnesium binding site 10 out of 10 in the Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg82

b:41.3
occ:0.50
 O B:HOH95 2.1 92.4 1.0
OP2 B:C67 2.5 43.7 1.0
O B:HOH96 2.5 50.2 1.0
P B:C67 3.9 38.7 1.0
O3' B:G66 4.4 44.0 1.0
O B:HOH146 4.4 58.6 1.0
O5' B:C67 4.8 32.7 1.0
OP1 B:C67 4.9 35.8 1.0

Reference:

S.Thore, C.Frick, N.Ban. Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch J.Am.Chem.Soc. V. 130 8116 2008.
ISSN: ISSN 0002-7863
PubMed: 18533652
DOI: 10.1021/JA801708E
Page generated: Wed Aug 14 12:20:00 2024

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