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Magnesium in PDB 3d2v: Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate

Protein crystallography data

The structure of Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate, PDB code: 3d2v was solved by S.Thore, C.Frick, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.790, 110.780, 55.750, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate (pdb code 3d2v). 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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate, PDB code: 3d2v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3d2v

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Magnesium binding site 1 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg78

b:30.5
occ:1.00
 O1A A:PYI84 2.3 22.9 1.0
O A:HOH341 2.4 28.9 1.0
O1B A:PYI84 2.4 29.8 1.0
O A:HOH96 2.4 25.0 1.0
O A:HOH98 2.4 25.0 1.0
O A:HOH94 2.5 31.1 1.0
PB A:PYI84 3.3 21.8 1.0
O3B A:PYI84 3.5 23.6 1.0
PA A:PYI84 3.6 25.2 1.0
N4 A:C65 3.7 24.9 1.0
O3A A:PYI84 3.9 23.9 1.0
C8 A:G60 4.0 30.4 1.0
O A:HOH101 4.0 24.1 1.0
O A:HOH187 4.2 33.7 1.0
O4 A:U63 4.2 29.7 1.0
O A:HOH148 4.2 26.2 1.0
O6 A:G64 4.2 22.3 1.0
N7 A:G64 4.4 27.1 1.0
OM7 A:PYI84 4.4 26.9 1.0
C4 A:U63 4.6 29.6 1.0
C5 A:U63 4.6 31.4 1.0
O2' A:G60 4.6 27.2 1.0
N9 A:G60 4.6 31.4 1.0
C4 A:C65 4.7 24.7 1.0
C1' A:G60 4.7 28.3 1.0
O A:HOH85 4.7 19.9 1.0
N7 A:G60 4.7 28.9 1.0
O2B A:PYI84 4.8 26.7 1.0
O2A A:PYI84 4.8 26.5 1.0
C2' A:G60 4.9 29.3 1.0
O A:HOH188 4.9 35.9 1.0
N3 A:C65 5.0 22.7 1.0

Magnesium binding site 2 out of 10 in 3d2v

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Magnesium binding site 2 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg79

b:40.7
occ:1.00
 OP1 A:C51 2.4 27.6 1.0
OP2 A:A52 2.4 31.8 1.0
O B:HOH98 2.5 31.5 1.0
O A:HOH108 2.5 30.4 1.0
O A:HOH88 2.5 26.7 1.0
O A:HOH345 2.5 41.4 1.0
P A:C51 3.5 28.0 1.0
OP2 A:C51 3.9 27.0 1.0
P A:A52 3.9 35.3 1.0
O A:HOH104 4.0 27.5 1.0
O A:HOH255 4.0 39.6 1.0
O A:HOH194 4.1 37.4 1.0
N1 B:A50 4.1 27.5 1.0
O A:HOH140 4.2 34.1 1.0
O A:HOH147 4.2 34.3 1.0
C2 B:A50 4.3 29.7 1.0
O A:HOH156 4.3 37.6 1.0
O A:HOH344 4.4 33.9 1.0
C3' A:C51 4.5 26.4 1.0
O5' A:C51 4.5 25.5 1.0
O3' A:C51 4.6 28.2 1.0
O3' A:A50 4.7 23.6 1.0
N7 A:A52 4.7 32.1 1.0
O5' A:A52 4.7 34.0 1.0
OP1 A:A52 4.8 35.0 1.0
O A:HOH177 4.8 36.2 1.0
C8 A:A52 4.9 31.3 1.0

Magnesium binding site 3 out of 10 in 3d2v

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Magnesium binding site 3 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg80

b:41.0
occ:1.00
 O A:HOH332 2.8 30.8 1.0
O A:HOH167 2.9 33.2 1.0
OP2 A:G42 2.9 30.0 1.0
C5' A:U41 3.3 38.1 1.0
O A:HOH331 3.5 52.0 1.0
O A:HOH378 3.5 33.5 1.0
C4' A:U41 4.0 38.4 1.0
N7 A:G42 4.1 28.7 1.0
P A:G42 4.4 29.9 1.0
OP2 A:U41 4.4 50.0 1.0
O5' A:U41 4.4 39.6 1.0
C8 A:G42 4.6 29.6 1.0
C3' A:U41 4.7 33.4 1.0
O3' A:U40 4.7 41.0 1.0
P A:U41 4.8 41.9 1.0
O3' A:U41 5.0 35.6 1.0

Magnesium binding site 4 out of 10 in 3d2v

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Magnesium binding site 4 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg81

b:24.9
occ:1.00
 O3B A:PYI84 2.2 23.6 1.0
O6 A:G48 2.2 18.5 1.0
O6 A:G66 2.3 22.5 1.0
O A:HOH339 2.4 20.8 1.0
O A:HOH89 2.4 21.3 1.0
O A:HOH85 2.5 19.9 1.0
C6 A:G48 3.3 21.0 1.0
C6 A:G66 3.3 24.8 1.0
PB A:PYI84 3.6 21.8 1.0
N1 A:G66 3.6 20.6 1.0
N1 A:G48 3.7 25.3 1.0
O A:HOH341 3.7 28.9 1.0
O4 A:U47 3.8 22.1 1.0
O A:HOH340 4.0 27.3 1.0
N1 A:A49 4.0 24.0 1.0
O3A A:PYI84 4.1 23.9 1.0
O2B A:PYI84 4.1 26.7 1.0
N3 A:C65 4.2 22.7 1.0
O A:HOH86 4.3 18.9 1.0
O2A A:PYI84 4.3 26.5 1.0
C2 A:A49 4.3 22.2 1.0
N7 A:G60 4.4 28.9 1.0
N4 A:C65 4.6 24.9 1.0
C5 A:G48 4.6 22.5 1.0
C5 A:G66 4.6 21.7 1.0
O1A A:PYI84 4.6 22.9 1.0
PA A:PYI84 4.6 25.2 1.0
O1B A:PYI84 4.7 29.8 1.0
C4 A:U47 4.7 22.6 1.0
C4 A:C65 4.8 24.7 1.0
C2 A:G66 5.0 24.5 1.0

Magnesium binding site 5 out of 10 in 3d2v

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Magnesium binding site 5 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg82

b:38.5
occ:1.00
 O A:HOH151 2.6 29.5 1.0
O A:HOH319 2.6 37.1 1.0
O A:HOH208 2.6 36.6 1.0
O A:HOH114 2.6 33.3 1.0
O A:HOH321 2.7 44.8 1.0
N7 A:A29 2.8 34.0 1.0
O A:HOH320 3.4 41.2 1.0
C8 A:A29 3.6 36.9 1.0
C5 A:A29 3.9 34.6 1.0
N6 A:A29 4.0 28.4 1.0
O A:HOH128 4.1 27.2 1.0
OP2 A:A44 4.2 27.0 1.0
O A:HOH379 4.3 42.7 1.0
C6 A:A29 4.4 30.6 1.0
O A:HOH237 4.4 43.4 1.0
O A:HOH226 4.5 41.4 1.0
O A:HOH380 4.5 53.6 1.0
O A:HOH322 4.5 42.7 1.0
O2' A:G28 4.5 34.7 1.0
O6 A:G30 4.7 28.1 1.0
O A:HOH174 4.7 28.8 1.0
O A:HOH137 4.8 35.0 1.0
O A:HOH293 4.8 44.5 1.0
N9 A:A29 4.9 36.4 1.0

Magnesium binding site 6 out of 10 in 3d2v

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Magnesium binding site 6 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg83

b:50.5
occ:1.00
 OP1 A:G48 2.9 29.6 1.0
O B:HOH118 2.9 32.2 1.0
O A:HOH258 2.9 41.8 1.0
O B:HOH296 2.9 41.2 1.0
O A:HOH107 3.0 30.7 1.0
O A:HOH278 3.1 42.9 1.0
O B:HOH295 3.5 56.9 1.0
O A:HOH338 3.7 27.5 1.0
O B:HOH233 3.8 41.6 1.0
O B:HOH230 3.9 36.8 1.0
O B:HOH293 4.0 37.9 1.0
P A:G48 4.1 24.3 1.0
OP1 B:C14 4.1 28.7 1.0
O3' A:U47 4.3 25.3 1.0
OP2 B:C14 4.4 30.7 1.0
OP2 B:U15 4.5 32.4 1.0
O A:HOH222 4.7 31.2 1.0
P B:C14 4.7 30.7 1.0
OP2 A:G48 4.9 25.1 1.0

Magnesium binding site 7 out of 10 in 3d2v

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Magnesium binding site 7 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg78

b:43.8
occ:1.00
 OP2 B:A52 2.4 30.2 1.0
O A:HOH102 2.5 30.9 1.0
O B:HOH300 2.5 45.0 1.0
O B:HOH88 2.5 36.6 1.0
O B:HOH111 2.6 29.8 1.0
OP1 B:C51 2.8 28.5 1.0
O B:HOH237 3.5 43.9 1.0
O B:HOH97 3.8 33.2 1.0
P B:A52 3.8 34.4 1.0
O B:HOH214 3.9 43.1 1.0
P B:C51 4.0 26.3 1.0
O B:HOH103 4.1 29.3 1.0
O B:HOH191 4.3 40.0 1.0
O B:HOH119 4.3 37.9 1.0
N7 B:A52 4.4 34.9 1.0
OP2 B:C51 4.4 27.6 1.0
O5' B:A52 4.4 33.7 1.0
O B:HOH301 4.4 37.5 1.0
N1 A:A50 4.6 33.2 1.0
C8 B:A52 4.6 34.4 1.0
OP1 B:A52 4.7 37.1 1.0
C3' B:C51 4.7 28.9 1.0
O3' B:C51 4.7 31.4 1.0
C2 A:A50 4.8 30.9 1.0
O5' B:C51 4.9 27.7 1.0

Magnesium binding site 8 out of 10 in 3d2v

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Magnesium binding site 8 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg79

b:31.8
occ:1.00
 O1A B:PYI82 2.4 25.7 1.0
O1B B:PYI82 2.4 33.7 1.0
O B:HOH315 2.4 28.3 1.0
O B:HOH316 2.4 24.8 1.0
O B:HOH180 2.4 29.3 1.0
O B:HOH87 2.5 29.2 1.0
PB B:PYI82 3.2 29.4 1.0
O3B B:PYI82 3.3 26.8 1.0
PA B:PYI82 3.6 29.8 1.0
N4 B:C65 3.9 30.2 1.0
O3A B:PYI82 3.9 27.4 1.0
O B:HOH96 3.9 27.2 1.0
O B:HOH196 4.0 32.7 1.0
C8 B:G60 4.0 29.8 1.0
O B:HOH106 4.2 31.4 1.0
O4 B:U63 4.2 32.2 1.0
OM7 B:PYI82 4.2 26.5 1.0
O6 B:G64 4.3 26.7 1.0
O B:HOH317 4.5 44.7 1.0
C5 B:U63 4.5 35.9 1.0
N7 B:G64 4.5 31.2 1.0
O2' B:G60 4.5 32.3 1.0
C4 B:U63 4.6 32.3 1.0
O B:HOH162 4.6 37.8 1.0
O B:HOH210 4.7 36.8 1.0
N9 B:G60 4.7 33.7 1.0
C1' B:G60 4.7 29.4 1.0
O2B B:PYI82 4.7 30.1 1.0
O B:HOH314 4.8 25.0 1.0
C4 B:C65 4.8 31.0 1.0
N7 B:G60 4.8 31.2 1.0
O2A B:PYI82 4.9 32.1 1.0
C2' B:G60 4.9 32.2 1.0

Magnesium binding site 9 out of 10 in 3d2v

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Magnesium binding site 9 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg80

b:28.2
occ:1.00
 O6 B:G48 2.3 22.4 1.0
O3B B:PYI82 2.3 26.8 1.0
O6 B:G66 2.3 26.7 1.0
O B:HOH89 2.4 25.7 1.0
O B:HOH83 2.4 23.8 1.0
O B:HOH314 2.5 25.0 1.0
C6 B:G66 3.3 27.6 1.0
C6 B:G48 3.3 26.7 1.0
PB B:PYI82 3.6 29.4 1.0
N1 B:G66 3.6 26.5 1.0
N1 B:G48 3.7 23.6 1.0
O4 B:U47 3.7 23.8 1.0
O3A B:PYI82 3.8 27.4 1.0
O B:HOH318 3.9 30.4 1.0
O2B B:PYI82 4.0 30.1 1.0
O B:HOH315 4.0 28.3 1.0
O B:HOH91 4.2 23.9 1.0
N1 B:A49 4.2 28.4 1.0
N3 B:C65 4.4 26.0 1.0
O2A B:PYI82 4.4 32.1 1.0
O1A B:PYI82 4.4 25.7 1.0
C2 B:A49 4.5 28.1 1.0
N7 B:G60 4.5 31.2 1.0
PA B:PYI82 4.5 29.8 1.0
C5 B:G48 4.6 24.9 1.0
C5 B:G66 4.6 26.7 1.0
C4 B:U47 4.7 27.4 1.0
N4 B:C65 4.7 30.2 1.0
O1B B:PYI82 4.8 33.7 1.0
O B:HOH122 4.8 37.2 1.0
O B:HOH104 4.8 25.5 1.0
C2 B:A43 4.8 27.4 1.0
C2 B:G66 4.9 30.9 1.0

Magnesium binding site 10 out of 10 in 3d2v

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Magnesium binding site 10 out of 10 in the Structure of the Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate


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 Eukaryotic Tpp-Specific Riboswitch Bound to the Antibacterial Compound Pyrithiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg81

b:39.4
occ:1.00
 O B:HOH172 2.6 37.5 1.0
O B:HOH127 2.6 34.2 1.0
O B:HOH90 2.6 29.3 1.0
O B:HOH182 2.7 38.9 1.0
N7 B:A29 2.7 36.4 1.0
O B:HOH181 3.2 30.0 1.0
C8 B:A29 3.6 37.3 1.0
C5 B:A29 3.8 36.7 1.0
N6 B:A29 3.9 35.2 1.0
O B:HOH173 4.2 33.4 1.0
C6 B:A29 4.3 36.7 1.0
O B:HOH167 4.4 36.8 1.0
O2' B:G28 4.4 37.0 1.0
O B:HOH193 4.6 34.9 1.0
O6 B:G30 4.6 31.0 1.0
OP2 B:A44 4.6 28.8 1.0
O B:HOH262 4.9 35.8 1.0
N9 B:A29 4.9 37.3 1.0
C4 B:A29 5.0 39.1 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 12:20:56 2024

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