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Magnesium in PDB 4ena: Crystal Structure of Fluoride Riboswitch, Soaked in Cs+

Protein crystallography data

The structure of Crystal Structure of Fluoride Riboswitch, Soaked in Cs+, PDB code: 4ena was solved by A.M.Ren, K.R.Rajashankar, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.742, 77.149, 42.477, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 26.4

Other elements in 4ena:

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

Fluorine (F) 1 atom
Caesium (Cs) 5 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 7 in 4ena

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Magnesium binding site 1 out of 7 in the Crystal Structure of Fluoride Riboswitch, Soaked in Cs+


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 Fluoride Riboswitch, Soaked in Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:58.1
occ:1.00
 O A:HOH211 2.1 52.1 1.0
O A:HOH208 2.2 57.1 1.0
O6 A:G29 2.7 52.3 1.0
C6 A:G29 3.5 48.1 1.0
N7 A:G29 3.6 48.5 1.0
C5 A:G29 3.9 47.1 1.0
N1 A:G29 4.6 44.4 1.0
O4 A:U28 4.7 46.8 1.0
C8 A:G29 4.8 48.6 1.0

Magnesium binding site 2 out of 7 in 4ena

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Magnesium binding site 2 out of 7 in the Crystal Structure of Fluoride Riboswitch, Soaked in Cs+


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

b:68.5
occ:1.00
 O3G A:GTP1 2.3 74.8 1.0
O2G A:GTP1 2.8 84.0 1.0
PG A:GTP1 3.0 84.3 1.0
O1G A:GTP1 3.3 79.3 1.0
O3B A:GTP1 4.5 83.1 1.0

Magnesium binding site 3 out of 7 in 4ena

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Magnesium binding site 3 out of 7 in the Crystal Structure of Fluoride Riboswitch, Soaked in Cs+


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 Fluoride Riboswitch, Soaked in Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:46.8
occ:1.00
 F A:F113 1.8 54.0 1.0
OP2 A:A6 2.0 52.6 1.0
OP1 A:U41 2.0 49.6 1.0
O A:HOH201 2.1 47.0 1.0
OP2 A:U7 2.1 47.0 1.0
OP2 A:G42 2.3 52.1 1.0
MG A:MG110 3.1 52.5 1.0
P A:G42 3.1 52.5 1.0
OP1 A:G42 3.1 55.4 1.0
P A:U7 3.2 43.6 1.0
P A:A6 3.3 50.5 1.0
P A:U41 3.4 44.8 1.0
MG A:MG109 3.5 53.2 1.0
OP1 A:U7 3.5 51.1 1.0
OP1 A:A6 3.8 53.8 1.0
C5' A:U41 4.0 52.6 1.0
O3' A:U41 4.0 54.0 1.0
O3' A:A6 4.0 51.3 1.0
O5' A:U41 4.0 51.5 1.0
O3' A:G5 4.3 56.2 1.0
C3' A:A6 4.3 50.2 1.0
OP2 A:U41 4.3 47.8 1.0
O5' A:A6 4.3 52.9 1.0
O3' A:A40 4.4 46.0 1.0
O5' A:G42 4.5 57.7 1.0
C3' A:U41 4.5 54.4 1.0
O A:HOH215 4.5 55.6 1.0
O5' A:U7 4.5 47.5 1.0
N2 A:G39 4.6 45.9 1.0
C5' A:A6 4.7 51.4 1.0
C4' A:U41 4.8 53.8 1.0
C5' A:G42 4.9 55.9 1.0

Magnesium binding site 4 out of 7 in 4ena

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Magnesium binding site 4 out of 7 in the Crystal Structure of Fluoride Riboswitch, Soaked in Cs+


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

b:53.2
occ:1.00
 F A:F113 1.9 54.0 1.0
O A:HOH219 2.0 57.8 1.0
OP1 A:A6 2.1 53.8 1.0
OP1 A:G42 2.2 55.4 1.0
MG A:MG110 3.1 52.5 1.0
P A:A6 3.1 50.5 1.0
O A:HOH215 3.3 55.6 1.0
OP2 A:A6 3.3 52.6 1.0
P A:G42 3.4 52.5 1.0
MG A:MG108 3.5 46.8 1.0
O3' A:U41 3.8 54.0 1.0
OP1 A:U7 3.9 51.1 1.0
O3' A:G5 3.9 56.2 1.0
C3' A:G5 4.1 58.3 1.0
OP2 A:G42 4.1 52.1 1.0
CS A:CS102 4.2 0.6 1.0
O5' A:A6 4.4 52.9 1.0
O5' A:G5 4.4 55.1 1.0
OP2 A:G5 4.5 56.7 1.0
OP2 A:U7 4.7 47.0 1.0
P A:U7 4.7 43.6 1.0
O5' A:G42 4.7 57.7 1.0
OP1 A:G5 4.8 60.1 1.0
P A:G5 4.8 53.7 1.0
O A:HOH218 4.8 60.2 1.0
OP2 A:G8 4.8 51.6 1.0
C5' A:G5 4.9 55.4 1.0
OP1 A:U41 5.0 49.6 1.0
C3' A:U41 5.0 54.4 1.0

Magnesium binding site 5 out of 7 in 4ena

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Magnesium binding site 5 out of 7 in the Crystal Structure of Fluoride Riboswitch, Soaked in Cs+


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 Fluoride Riboswitch, Soaked in Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg110

b:52.5
occ:1.00
 F A:F113 1.9 54.0 1.0
OP2 A:G8 2.5 51.6 1.0
OP1 A:U7 2.6 51.1 1.0
MG A:MG108 3.1 46.8 1.0
MG A:MG109 3.1 53.2 1.0
OP1 A:U41 3.4 49.6 1.0
P A:U7 3.5 43.6 1.0
OP2 A:U7 3.5 47.0 1.0
C5' A:U41 3.8 52.6 1.0
P A:G8 4.0 55.6 1.0
O2' A:A40 4.2 44.1 1.0
O A:HOH215 4.2 55.6 1.0
OP2 A:A6 4.3 52.6 1.0
OP1 A:A6 4.3 53.8 1.0
O5' A:U7 4.4 47.5 1.0
P A:U41 4.4 44.8 1.0
OP1 A:G42 4.4 55.4 1.0
O3' A:A40 4.4 46.0 1.0
O A:HOH218 4.6 60.2 1.0
O5' A:U41 4.6 51.5 1.0
OP2 A:G42 4.6 52.1 1.0
C3' A:U7 4.7 48.4 1.0
OP1 A:G8 4.8 53.4 1.0
C4' A:U41 4.8 53.8 1.0
O3' A:A6 4.8 51.3 1.0
O5' A:G8 4.8 51.0 1.0
O3' A:U41 4.8 54.0 1.0
O A:HOH219 4.8 57.8 1.0
P A:G42 4.8 52.5 1.0
O3' A:U7 4.8 50.4 1.0
P A:A6 4.9 50.5 1.0
O A:HOH201 5.0 47.0 1.0

Magnesium binding site 6 out of 7 in 4ena

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Magnesium binding site 6 out of 7 in the Crystal Structure of Fluoride Riboswitch, Soaked in Cs+


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 Fluoride Riboswitch, Soaked in Cs+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg111

b:51.5
occ:1.00
 O A:HOH205 2.0 43.9 1.0
O A:HOH202 2.1 43.4 1.0
OP2 A:A40 2.1 48.6 1.0
O A:HOH203 2.1 43.7 1.0
O A:HOH204 2.1 49.6 1.0
P A:A40 3.3 49.8 1.0
O5' A:A40 3.5 46.8 1.0
O2 A:C50 3.8 49.7 1.0
C3' A:G39 4.3 50.6 1.0
O5' A:G39 4.3 55.0 1.0
O3' A:G39 4.3 51.3 1.0
OP2 A:G39 4.3 57.2 1.0
OP1 A:A40 4.3 49.5 1.0
O4 A:U7 4.4 45.0 1.0
N3 A:C50 4.5 49.5 1.0
C2 A:C50 4.6 50.4 1.0
P A:G39 4.7 62.7 1.0
N1 A:A49 4.7 42.9 1.0
OP1 A:G39 4.8 60.2 1.0
C5' A:A40 4.9 46.3 1.0
C5' A:G39 4.9 52.2 1.0

Magnesium binding site 7 out of 7 in 4ena

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Magnesium binding site 7 out of 7 in the Crystal Structure of Fluoride Riboswitch, Soaked in Cs+


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

b:76.0
occ:1.00
 O A:HOH217 2.1 63.4 1.0
O A:HOH210 2.2 65.3 1.0
O6 A:G11 3.7 72.8 1.0
O6 A:G10 3.7 68.0 1.0
O6 A:G43 3.9 69.7 1.0
CS A:CS102 4.1 0.6 1.0
O2' A:U41 4.2 60.1 1.0
N4 A:C12 4.2 72.2 1.0
N4 A:C44 4.3 69.5 1.0
C6 A:G10 4.6 66.9 1.0
N7 A:G10 4.6 61.1 1.0
C6 A:G11 4.8 71.0 1.0
C5 A:G10 5.0 64.5 1.0

Reference:

A.Ren, K.R.Rajashankar, D.J.Patel. Fluoride Ion Encapsulation By MG2+ Ions and Phosphates in A Fluoride Riboswitch. Nature V. 486 85 2012.
ISSN: ISSN 0028-0836
PubMed: 22678284
DOI: 10.1038/NATURE11152
Page generated: Mon Aug 11 12:27:07 2025

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