Atomistry » Magnesium » PDB 4egw-4eqx » 4en5
Atomistry »
  Magnesium »
    PDB 4egw-4eqx »
      4en5 »

Magnesium in PDB 4en5: Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked

Protein crystallography data

The structure of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked, PDB code: 4en5 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) 19.36 / 2.96
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.205, 77.287, 42.597, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.1

Other elements in 4en5:

The structure of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked also contains other interesting chemical elements:

Fluorine (F) 1 atom
Thallium (Tl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked (pdb code 4en5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked, PDB code: 4en5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 1 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:60.6
occ:1.00
 O A:HOH206 2.1 61.8 1.0
O A:HOH204 2.1 70.8 1.0
O A:HOH205 2.1 70.4 1.0
O6 A:G29 2.5 70.5 1.0
C6 A:G29 3.1 64.7 1.0
N7 A:G29 3.4 64.5 1.0
C5 A:G29 3.5 60.8 1.0
N1 A:G29 4.2 62.2 1.0
C8 A:G29 4.6 64.9 1.0
C4 A:G29 4.7 60.9 1.0
OP2 A:A31 4.8 62.0 1.0

Magnesium binding site 2 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 2 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:60.4
occ:1.00
 F A:F110 1.8 67.4 1.0
OP2 A:G42 2.0 62.4 1.0
O A:HOH217 2.0 57.6 1.0
OP1 A:U41 2.0 61.9 1.0
OP2 A:A6 2.1 66.5 1.0
OP2 A:U7 2.1 59.2 1.0
MG A:MG103 2.7 61.7 1.0
P A:G42 2.9 61.8 1.0
O A:HOH215 3.0 60.5 1.0
O A:HOH214 3.0 65.9 1.0
OP1 A:G42 3.1 64.8 1.0
P A:A6 3.2 58.3 1.0
P A:U7 3.2 56.2 1.0
OP1 A:A6 3.4 65.5 1.0
P A:U41 3.4 56.5 1.0
MG A:MG104 3.5 72.4 1.0
OP1 A:U7 3.5 67.2 1.0
O A:HOH203 3.7 66.1 1.0
O3' A:U41 3.7 66.3 1.0
C5' A:U41 4.0 64.0 1.0
O5' A:U41 4.0 61.0 1.0
O3' A:A6 4.1 63.1 1.0
O3' A:G5 4.2 67.1 1.0
C3' A:U41 4.3 66.1 1.0
O5' A:G42 4.3 68.9 1.0
OP2 A:U41 4.3 61.6 1.0
O5' A:A6 4.3 60.9 1.0
C3' A:A6 4.4 62.2 1.0
O5' A:U7 4.4 56.5 1.0
O3' A:A40 4.5 57.8 1.0
C4' A:U41 4.6 65.6 1.0
N2 A:G39 4.7 61.5 1.0
C5' A:G42 4.8 70.4 1.0
OP2 A:G8 4.8 60.2 1.0
TL A:TL116 4.8 0.6 1.0
C5' A:A6 4.9 65.7 1.0

Magnesium binding site 3 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 3 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:61.7
occ:1.00
 F A:F110 1.8 67.4 1.0
O A:HOH214 2.0 65.9 1.0
O A:HOH215 2.1 60.5 1.0
O A:HOH203 2.1 66.1 1.0
OP1 A:U7 2.2 67.2 1.0
OP2 A:G8 2.4 60.2 1.0
MG A:MG102 2.7 60.4 1.0
MG A:MG104 2.9 72.4 1.0
P A:U7 3.0 56.2 1.0
OP2 A:U7 3.0 59.2 1.0
OP1 A:U41 3.5 61.9 1.0
P A:G8 3.6 62.9 1.0
OP1 A:A6 3.7 65.5 1.0
O5' A:U7 4.0 56.5 1.0
TL A:TL116 4.0 0.6 1.0
OP1 A:G8 4.0 61.5 1.0
OP2 A:A6 4.0 66.5 1.0
OP1 A:G42 4.3 64.8 1.0
O3' A:A6 4.3 63.1 1.0
OP2 A:G42 4.3 62.4 1.0
C5' A:U41 4.4 64.0 1.0
P A:A6 4.4 58.3 1.0
O A:HOH217 4.5 57.6 1.0
O3' A:U7 4.6 61.4 1.0
C3' A:U7 4.6 59.0 1.0
P A:G42 4.7 61.8 1.0
O5' A:G8 4.7 60.5 1.0
P A:U41 4.7 56.5 1.0
O3' A:U41 4.8 66.3 1.0
O A:HOH226 4.8 81.5 1.0
C5' A:U7 4.8 61.2 1.0
O2' A:A40 4.9 56.3 1.0
O3' A:A40 4.9 57.8 1.0
O A:HOH202 5.0 68.2 1.0

Magnesium binding site 4 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 4 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:72.4
occ:1.00
 F A:F110 1.9 67.4 1.0
O A:HOH214 2.1 65.9 1.0
O A:HOH203 2.2 66.1 1.0
O A:HOH226 2.2 81.5 1.0
OP1 A:G42 2.3 64.8 1.0
OP1 A:A6 2.3 65.5 1.0
MG A:MG103 2.9 61.7 1.0
P A:G42 3.3 61.8 1.0
MG A:MG102 3.5 60.4 1.0
P A:A6 3.5 58.3 1.0
O3' A:U41 3.6 66.3 1.0
OP2 A:A6 3.9 66.5 1.0
OP2 A:G42 4.0 62.4 1.0
OP1 A:U7 4.0 67.2 1.0
O3' A:G5 4.2 67.1 1.0
TL A:TL116 4.3 0.6 1.0
O5' A:G5 4.3 63.3 1.0
C3' A:G5 4.3 72.4 1.0
OP2 A:G5 4.4 67.7 1.0
O A:HOH215 4.7 60.5 1.0
O5' A:G42 4.7 68.9 1.0
OP2 A:U7 4.7 59.2 1.0
O5' A:A6 4.7 60.9 1.0
P A:G5 4.8 64.2 1.0
C3' A:U41 4.8 66.1 1.0
P A:U7 4.9 56.2 1.0
TL A:TL113 4.9 0.6 1.0
OP2 A:G8 4.9 60.2 1.0

Magnesium binding site 5 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 5 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:78.8
occ:1.00
 O A:HOH216 2.1 77.2 1.0
O A:HOH234 3.0 79.0 1.0
O6 A:G2 3.2 82.3 1.0
N7 A:G2 3.3 78.0 1.0
C6 A:G2 3.8 79.6 1.0
C5 A:G2 3.8 78.4 1.0
C8 A:G2 4.4 79.2 1.0
O A:HOH233 4.9 98.5 1.0

Magnesium binding site 6 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 6 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:53.5
occ:1.00
 N7 A:G34 2.0 56.9 1.0
O A:HOH208 2.1 67.1 1.0
O A:HOH209 2.1 52.7 1.0
C8 A:G34 2.9 56.4 1.0
TL A:TL115 3.1 0.1 1.0
C5 A:G34 3.1 53.7 1.0
N7 A:A33 3.5 55.1 1.0
C5 A:A33 3.6 55.1 1.0
O6 A:G34 3.6 58.0 1.0
C6 A:G34 3.7 54.5 1.0
C6 A:A33 3.9 53.0 1.0
C8 A:A33 4.0 53.4 1.0
N9 A:G34 4.1 54.8 1.0
N6 A:A33 4.1 51.1 1.0
C4 A:A33 4.1 54.1 1.0
C4 A:G34 4.2 54.9 1.0
N9 A:A33 4.4 53.5 1.0
O A:HOH229 4.5 64.7 1.0
N1 A:A33 4.7 56.1 1.0
OP2 A:G34 4.7 59.2 1.0
O A:HOH230 4.8 61.7 1.0
N7 A:G35 4.8 57.8 1.0
O6 A:G35 4.9 57.3 1.0
N3 A:A33 4.9 53.6 1.0

Magnesium binding site 7 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 7 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:54.6
occ:1.00
 O A:HOH207 2.1 69.3 1.0
O6 A:G36 2.3 54.7 1.0
O A:HOH229 2.7 64.7 1.0
O A:HOH230 2.8 61.7 1.0
N7 A:G36 3.0 57.3 1.0
C6 A:G36 3.1 56.6 1.0
TL A:TL115 3.2 0.1 1.0
C5 A:G36 3.4 57.2 1.0
O6 A:G35 3.4 57.3 1.0
C6 A:G35 4.0 56.5 1.0
C8 A:G36 4.3 57.5 1.0
N4 A:C37 4.3 59.5 1.0
N1 A:G36 4.5 56.4 1.0
C5 A:G35 4.5 56.4 1.0
N7 A:G35 4.6 57.8 1.0
C4 A:G36 4.8 57.0 1.0
N1 A:G35 4.8 55.8 1.0
N4 A:C26 5.0 58.4 1.0

Magnesium binding site 8 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 8 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:77.4
occ:1.00
 OP1 A:C50 3.1 88.5 1.0
N7 A:G52 3.3 79.3 1.0
O6 A:G52 3.8 76.1 1.0
C5 A:G52 4.2 77.0 1.0
C8 A:G52 4.2 78.8 1.0
P A:C50 4.3 87.7 1.0
C6 A:G52 4.4 76.5 1.0
O5' A:C50 4.6 76.2 1.0
OP2 A:C50 4.9 72.1 1.0
C5' A:C50 5.0 75.2 1.0

Magnesium binding site 9 out of 9 in 4en5

Go back to Magnesium Binding Sites List in 4en5
Magnesium binding site 9 out of 9 in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:54.5
occ:1.00
 O A:HOH212 2.1 62.4 1.0
O A:HOH210 2.1 55.4 1.0
O A:HOH211 2.1 55.8 1.0
O A:HOH213 2.1 56.1 1.0
OP2 A:A40 2.3 60.6 1.0
O5' A:A40 2.5 56.7 1.0
P A:A40 2.9 58.3 1.0
C5' A:A40 3.8 58.1 1.0
OP1 A:A40 3.9 59.2 1.0
O4 A:U7 3.9 57.5 1.0
O4' A:A40 4.0 51.2 1.0
O3' A:G39 4.1 57.9 1.0
N1 A:A49 4.2 55.8 1.0
C3' A:G39 4.3 62.7 1.0
C4' A:A40 4.3 55.9 1.0
N6 A:A49 4.4 58.4 1.0
N3 A:C50 4.4 60.0 1.0
C6 A:A49 4.8 58.7 1.0
O2 A:C50 4.8 64.5 1.0
O5' A:G39 4.9 63.7 1.0
C4 A:U7 5.0 55.4 1.0
O A:HOH222 5.0 69.3 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: Fri Aug 16 14:32:05 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy