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Magnesium in PDB 3oxe: Crystal Structure of Glycine Riboswitch, MN2+ Soaked

Protein crystallography data

The structure of Crystal Structure of Glycine Riboswitch, MN2+ Soaked, PDB code: 3oxe was solved by L.Huang, A.Serganov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.708, 83.708, 198.958, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 21.9

Other elements in 3oxe:

The structure of Crystal Structure of Glycine Riboswitch, MN2+ Soaked also contains other interesting chemical elements:

Manganese (Mn) 32 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked (pdb code 3oxe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked, PDB code: 3oxe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3oxe

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Magnesium binding site 1 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg133

b:0.9
occ:1.00
 O A:HOH146 2.2 73.7 1.0
O A:HOH148 2.2 73.6 1.0
O A:HOH145 2.2 73.7 1.0
O A:HOH143 2.2 73.3 1.0
O A:HOH147 2.2 73.5 1.0
O A:HOH144 2.2 73.2 1.0
O6 A:G25 4.3 88.6 1.0
O6 A:G26 4.4 92.2 1.0
N7 A:G25 4.4 90.4 1.0
N7 A:G26 4.4 95.8 1.0
O4 A:U27 4.8 90.7 1.0
C6 A:G25 4.9 90.2 1.0
C5 A:G25 5.0 91.1 1.0

Magnesium binding site 2 out of 10 in 3oxe

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Magnesium binding site 2 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg134

b:95.5
occ:1.00
 O A:HOH149 2.2 72.9 1.0
O B:HOH143 2.2 72.8 1.0
O B:HOH146 2.2 73.2 1.0
O B:HOH142 2.2 73.0 1.0
O B:HOH144 2.2 72.7 1.0
O B:HOH145 2.2 72.9 1.0
OP1 B:U67 4.2 57.1 1.0
OP1 A:G10 4.4 54.1 1.0
OP2 B:U67 4.4 56.9 1.0
OP2 B:G32 4.5 50.8 1.0
OP2 B:C68 4.6 57.5 1.0
P B:U67 4.8 57.3 1.0
O3' A:A9 5.0 54.6 1.0

Magnesium binding site 3 out of 10 in 3oxe

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Magnesium binding site 3 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg135

b:74.8
occ:1.00
 OP2 A:A21 2.2 62.5 1.0
O A:HOH152 2.2 42.2 1.0
O A:HOH150 2.2 41.8 1.0
O A:HOH151 2.2 42.3 1.0
O A:HOH153 2.2 41.5 1.0
O A:HOH154 2.2 42.1 1.0
P A:A21 3.6 62.1 1.0
N6 A:A22 4.0 72.5 1.0
O5' A:A21 4.2 60.7 1.0
N7 A:A22 4.2 68.8 1.0
O4 A:U23 4.3 73.1 1.0
N7 A:A21 4.3 61.2 1.0
O2 A:U19 4.4 78.2 1.0
OP1 A:A21 4.4 62.6 1.0
C5' A:U20 4.5 66.0 1.0
C3' A:U20 4.6 62.7 1.0
O3' A:U20 4.6 61.9 1.0
C8 A:A21 4.6 59.9 1.0
O5' A:U20 4.9 67.9 1.0
C6 A:A22 4.9 71.7 1.0
O2' A:U19 4.9 74.9 1.0
C5 A:A22 4.9 70.0 1.0
O3' A:U19 5.0 72.0 1.0

Magnesium binding site 4 out of 10 in 3oxe

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Magnesium binding site 4 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg136

b:91.4
occ:1.00
 OP2 B:A52 2.1 79.0 1.0
P B:A52 3.6 79.0 1.0
O6 B:G49 4.0 75.9 1.0
N7 B:G49 4.1 76.9 1.0
O5' B:A52 4.2 78.4 1.0
N7 B:A52 4.4 79.3 1.0
OP1 B:A52 4.5 80.3 1.0
C8 B:A52 4.5 79.5 1.0
O3' B:A51 4.6 79.5 1.0
OP2 B:A51 4.6 77.8 1.0
N4 B:C48 4.6 80.7 1.0
C3' B:A51 4.6 78.9 1.0
C6 B:G49 4.7 75.5 1.0
C5 B:G49 4.7 75.7 1.0
C5 B:C48 4.9 81.7 1.0
C4 B:C48 4.9 80.9 1.0

Magnesium binding site 5 out of 10 in 3oxe

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Magnesium binding site 5 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg137

b:0.0
occ:1.00
 MN A:MN131 3.9 0.2 1.0
O6 A:G84 4.1 74.3 1.0
N7 A:G84 4.2 74.1 1.0
N7 A:A83 4.3 67.2 1.0
N6 A:A83 4.5 67.9 1.0
N6 A:A85 4.6 83.9 1.0
C5 A:A83 4.7 67.1 1.0
C6 A:G84 4.9 74.2 1.0
C6 A:A83 4.9 67.4 1.0
C5 A:G84 4.9 74.1 1.0

Magnesium binding site 6 out of 10 in 3oxe

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Magnesium binding site 6 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg138

b:0.9
occ:1.00
 MN B:MN119 3.7 0.3 1.0
OP2 B:A11 3.7 52.6 1.0
N7 B:A11 4.7 54.1 1.0
C8 B:A11 4.8 53.9 1.0
P B:A11 5.0 52.6 1.0

Magnesium binding site 7 out of 10 in 3oxe

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Magnesium binding site 7 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg139

b:0.1
occ:1.00
 O6 B:G47 4.0 88.1 1.0
O4 B:U46 4.0 94.5 1.0
C4 B:U46 4.6 95.1 1.0
C5 B:U46 4.6 96.0 1.0
N7 B:G47 4.9 89.6 1.0
C6 B:G47 5.0 88.0 1.0

Magnesium binding site 8 out of 10 in 3oxe

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Magnesium binding site 8 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg140

b:0.5
occ:1.00
 OP2 B:A59 3.9 0.5 1.0
O4 B:U61 4.1 88.0 1.0
O6 B:G62 4.1 81.2 1.0
N7 B:G60 4.4 96.8 1.0
N7 B:A59 4.4 0.9 1.0
N1 B:G62 4.6 79.9 1.0
OP2 B:A40 4.6 72.0 1.0
C6 B:G62 4.6 80.7 1.0
C8 B:A59 4.8 0.7 1.0

Magnesium binding site 9 out of 10 in 3oxe

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Magnesium binding site 9 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg141

b:0.2
occ:1.00
 N7 B:A37 3.5 70.0 1.0
OP2 B:A37 4.0 74.0 1.0
C8 B:A37 4.1 70.3 1.0
C5 B:A37 4.3 69.0 1.0
N6 B:A37 4.6 67.9 1.0
N7 B:G38 4.6 69.8 1.0
C6 B:A37 4.8 68.1 1.0
OP2 B:A64 4.8 64.4 1.0

Magnesium binding site 10 out of 10 in 3oxe

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Magnesium binding site 10 out of 10 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg142

b:70.6
occ:1.00
 OP2 A:A41 3.9 63.5 1.0
O6 A:G60 4.4 93.1 1.0
OP2 A:A40 4.5 67.7 1.0
O4 A:U61 4.6 85.7 1.0
O6 A:G42 4.9 70.6 1.0

Reference:

L.Huang, A.Serganov, D.J.Patel. Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026
Page generated: Thu Aug 15 08:45:31 2024

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