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Magnesium in PDB 3oxj: Crystal Structure of Glycine Riboswitch, Soaked in BA2+

Protein crystallography data

The structure of Crystal Structure of Glycine Riboswitch, Soaked in BA2+, PDB code: 3oxj 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 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.215, 84.215, 201.382, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 22.4

Other elements in 3oxj:

The structure of Crystal Structure of Glycine Riboswitch, Soaked in BA2+ also contains other interesting chemical elements:

Barium (Ba) 24 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+ (pdb code 3oxj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+, PDB code: 3oxj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in 3oxj

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Magnesium binding site 1 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:86.7
occ:1.00
OP2 A:G35 1.9 95.1 1.0
OP1 A:A34 2.1 92.4 1.0
O A:HOH127 2.2 60.2 1.0
O A:HOH128 2.2 59.5 1.0
O A:HOH126 2.2 60.0 1.0
O A:HOH125 2.2 59.9 1.0
P A:G35 3.3 96.3 1.0
P A:A34 3.5 92.1 1.0
OP1 A:G35 4.0 96.4 1.0
O5' A:A34 4.0 93.0 1.0
CA A:GLY89 4.1 92.6 1.0
O5' A:G35 4.2 97.8 1.0
O3' A:A34 4.2 95.8 1.0
O3' A:A33 4.3 90.4 1.0
C4' A:A33 4.3 89.9 1.0
C5' A:A34 4.4 93.0 1.0
N7 A:G35 4.4 97.9 1.0
OP2 A:A34 4.6 92.8 1.0
C3' A:A34 4.6 95.8 1.0
C8 A:G35 4.7 98.3 1.0
C3' A:A33 4.8 90.0 1.0
C5' A:A33 4.9 89.2 1.0
N7 A:G36 5.0 97.0 1.0
N A:GLY89 5.0 93.7 1.0

Magnesium binding site 2 out of 21 in 3oxj

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Magnesium binding site 2 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:0.3
occ:1.00
O A:HOH131 2.2 82.6 1.0
O A:HOH129 2.2 83.2 1.0
O A:HOH130 2.2 82.9 1.0
OP2 A:A33 2.2 87.8 1.0
OP2 A:C66 2.3 89.4 1.0
O2' A:G32 2.6 87.8 1.0
C2' A:G32 3.4 87.5 1.0
P A:A33 3.6 87.5 1.0
OXT A:GLY89 3.7 91.1 1.0
C3' A:G32 3.7 86.4 1.0
P A:C66 3.8 89.0 1.0
O3' A:G32 4.0 86.9 1.0
O4 A:U69 4.2 92.5 1.0
OP1 A:A33 4.5 86.5 1.0
OP1 A:C66 4.6 88.5 1.0
O3' A:A65 4.6 89.8 1.0
O5' A:C66 4.6 88.5 1.0
O5' A:A33 4.6 87.6 1.0
C5' A:A33 4.6 89.2 1.0
OP2 A:U67 4.7 88.5 1.0
C A:GLY89 4.8 91.9 1.0
C1' A:G32 4.8 87.7 1.0
C5 A:U67 4.8 92.2 1.0
C4' A:A65 4.9 88.7 1.0
O4 A:U67 5.0 92.6 1.0

Magnesium binding site 3 out of 21 in 3oxj

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Magnesium binding site 3 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:90.8
occ:1.00
OP1 A:A75 2.2 92.8 1.0
OP2 A:A76 2.3 92.5 1.0
OP1 A:C74 2.7 96.1 1.0
P A:A75 3.6 93.7 1.0
P A:A76 3.7 92.2 1.0
C5' A:C74 4.0 94.4 1.0
P A:C74 4.1 97.1 1.0
N6 A:A77 4.1 97.2 1.0
N7 A:A77 4.1 94.9 1.0
N6 A:A78 4.2 89.0 1.0
OP2 A:A75 4.2 95.2 1.0
O5' A:A76 4.3 92.6 1.0
N7 A:A76 4.3 95.2 1.0
O5' A:C74 4.4 96.4 1.0
O5' A:A75 4.4 93.8 1.0
C8 A:A76 4.6 94.5 1.0
O3' A:A75 4.6 92.1 1.0
O3' A:C74 4.6 93.5 1.0
C3' A:A75 4.7 92.8 1.0
OP1 A:A76 4.7 91.9 1.0
O3' A:G73 4.9 96.6 1.0
C5 A:A77 4.9 95.8 1.0
C6 A:A78 4.9 89.6 1.0
C5' A:A75 4.9 93.4 1.0
C6 A:A77 5.0 96.9 1.0
C4' A:C74 5.0 93.8 1.0

Magnesium binding site 4 out of 21 in 3oxj

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Magnesium binding site 4 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:0.1
occ:1.00
O B:HOH125 2.2 97.4 1.0
O A:HOH132 2.2 97.3 1.0
O A:HOH134 2.2 96.9 1.0
O A:HOH135 2.2 97.1 1.0
O A:HOH136 2.2 96.9 1.0
O A:HOH133 2.2 97.2 1.0
OP1 A:U67 4.4 88.7 1.0
OP1 B:G10 4.5 79.7 1.0
OP2 A:U67 4.7 88.5 1.0
OP2 A:C68 4.7 92.7 1.0
OP2 A:G32 4.7 87.1 1.0

Magnesium binding site 5 out of 21 in 3oxj

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Magnesium binding site 5 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg108

b:0.6
occ:1.00
O B:HOH130 2.2 0.5 1.0
O B:HOH128 2.2 0.3 1.0
O B:HOH129 2.2 0.1 1.0
O B:HOH126 2.2 0.3 1.0
O B:HOH127 2.2 0.3 1.0
O A:HOH137 2.2 0.2 1.0
OP2 B:G32 4.3 80.8 1.0
OP1 B:U67 4.4 86.0 1.0
OP2 B:C68 4.7 85.5 1.0

Magnesium binding site 6 out of 21 in 3oxj

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Magnesium binding site 6 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:93.4
occ:1.00
O A:HOH139 2.2 48.6 1.0
O A:HOH141 2.2 48.2 1.0
O A:HOH140 2.2 48.2 1.0
O A:HOH138 2.2 48.8 1.0
O A:HOH143 2.2 48.2 1.0
O A:HOH142 2.2 48.6 1.0
O4 A:U46 4.5 0.3 1.0
N4 A:C54 4.6 94.7 1.0
O6 A:G47 4.7 0.5 1.0
N4 A:C48 4.8 0.7 1.0
O6 A:G55 4.9 0.9 1.0

Magnesium binding site 7 out of 21 in 3oxj

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Magnesium binding site 7 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg110

b:79.8
occ:1.00
OP2 B:G35 2.0 89.0 1.0
OP1 B:A34 2.1 82.8 1.0
O B:HOH131 2.2 56.0 1.0
O B:HOH133 2.2 55.6 1.0
O B:HOH134 2.2 55.6 1.0
O B:HOH132 2.2 56.1 1.0
P B:G35 3.4 89.9 1.0
P B:A34 3.5 82.9 1.0
OP1 B:G35 4.1 90.1 1.0
O5' B:A34 4.1 83.8 1.0
O5' B:G35 4.2 90.8 1.0
CA B:GLY89 4.3 91.8 1.0
C4' B:A33 4.4 81.4 1.0
C5' B:A34 4.4 85.1 1.0
OP2 B:A34 4.4 82.8 1.0
O3' B:A33 4.5 82.2 1.0
O3' B:A34 4.5 89.0 1.0
N7 B:G35 4.5 93.5 1.0
N7 B:G36 4.7 89.1 1.0
C8 B:G35 4.7 93.4 1.0
C5' B:A33 4.8 80.9 1.0
C3' B:A34 4.8 88.0 1.0
C3' B:A33 4.8 81.5 1.0
O6 B:G36 5.0 87.5 1.0

Magnesium binding site 8 out of 21 in 3oxj

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Magnesium binding site 8 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg111

b:97.3
occ:1.00
OP2 B:A33 2.1 81.1 1.0
O B:HOH136 2.2 75.0 1.0
O B:HOH135 2.2 75.7 1.0
O B:HOH137 2.2 76.0 1.0
OP2 B:C66 2.3 88.1 1.0
O2' B:G32 2.4 80.7 1.0
C2' B:G32 3.2 80.8 1.0
P B:A33 3.4 80.2 1.0
O B:GLY89 3.6 91.5 1.0
C3' B:G32 3.6 80.1 1.0
P B:C66 3.8 88.8 1.0
O3' B:G32 3.9 79.9 1.0
O4 B:U69 4.3 90.8 1.0
OP1 B:A33 4.3 80.5 1.0
O5' B:A33 4.6 80.4 1.0
C B:GLY89 4.6 91.5 1.0
OP1 B:C66 4.6 88.1 1.0
C1' B:G32 4.6 81.7 1.0
O5' B:C66 4.7 88.5 1.0
C5' B:A33 4.7 80.9 1.0
O3' B:A65 4.7 88.9 1.0
OXT B:GLY89 4.7 91.4 1.0
C5 B:U67 4.7 91.0 1.0
OP2 B:U67 4.7 86.2 1.0
O4 B:U67 4.7 92.0 1.0
C4' B:A65 4.8 87.7 1.0
C5' B:A65 4.9 87.0 1.0

Magnesium binding site 9 out of 21 in 3oxj

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Magnesium binding site 9 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg112

b:1.0
occ:1.00
O A:HOH147 2.2 79.5 1.0
O A:HOH148 2.2 79.9 1.0
O A:HOH144 2.2 79.5 1.0
O A:HOH145 2.2 79.5 1.0
O A:HOH146 2.2 80.0 1.0
N7 A:G50 2.4 88.9 1.0
C8 A:G50 3.3 88.5 1.0
C5 A:G50 3.4 87.0 1.0
O6 A:G50 3.5 87.5 1.0
C6 A:G50 3.8 86.3 1.0
N7 A:G49 4.0 96.1 1.0
N9 A:G50 4.6 87.0 1.0
C4 A:G50 4.6 85.9 1.0
C8 A:G49 4.6 96.7 1.0
C5 A:G49 5.0 94.0 1.0

Magnesium binding site 10 out of 21 in 3oxj

Go back to Magnesium Binding Sites List in 3oxj
Magnesium binding site 10 out of 21 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg113

b:0.4
occ:1.00
OP1 A:A21 3.0 93.5 1.0
OP2 A:U20 3.2 0.3 1.0
O5' A:U20 3.7 0.6 1.0
P A:A21 4.1 93.0 1.0
P A:U20 4.1 0.9 1.0
O3' A:U20 4.1 92.2 1.0
OP2 A:C15 4.3 0.1 1.0
O3' A:U19 4.5 0.8 1.0
O2' A:A13 4.6 95.8 1.0
OP2 A:A21 4.9 94.7 1.0
C5' A:U20 5.0 97.1 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: Mon Dec 14 08:38:02 2020

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