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Magnesium in PDB 4enc: Crystal Structure of Fluoride Riboswitch

Protein crystallography data

The structure of Crystal Structure of Fluoride Riboswitch, PDB code: 4enc 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) 28.50 / 2.27
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.010, 75.223, 42.905, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 25.2

Other elements in 4enc:

The structure of Crystal Structure of Fluoride Riboswitch also contains other interesting chemical elements:

Fluorine (F) 1 atom
Potassium (K) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 4enc

Go back to Magnesium Binding Sites List in 4enc
Magnesium binding site 1 out of 5 in the Crystal Structure of Fluoride Riboswitch


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:42.9
occ:1.00
F A:F106 1.9 37.5 1.0
OP2 A:G8 2.0 53.6 1.0
O A:HOH204 2.0 36.6 1.0
O A:HOH205 2.1 41.2 1.0
O A:HOH203 2.1 40.0 1.0
OP1 A:U7 2.1 38.5 1.0
MG A:MG104 2.9 38.1 1.0
P A:U7 3.1 46.6 1.0
OP2 A:U7 3.4 39.3 1.0
P A:G8 3.4 55.0 1.0
O A:HOH208 3.5 42.2 1.0
MG A:MG103 3.5 54.3 1.0
K A:K107 3.6 75.4 1.0
OP1 A:U41 3.8 44.0 1.0
O5' A:U7 4.0 53.3 1.0
C3' A:U7 4.1 48.1 1.0
OP1 A:A6 4.1 48.0 1.0
O3' A:U7 4.1 52.7 1.0
OP1 A:G8 4.2 52.1 1.0
O A:HOH206 4.4 46.6 1.0
O2' A:A40 4.4 58.4 1.0
O3' A:A6 4.4 45.4 1.0
O5' A:G8 4.5 57.0 1.0
O A:HOH207 4.5 48.5 1.0
OP2 A:A6 4.5 43.6 1.0
C5' A:U41 4.6 45.9 1.0
O3' A:A40 4.6 49.3 1.0
OP1 A:G42 4.6 40.6 1.0
C5' A:U7 4.7 44.8 1.0
P A:U41 4.8 50.2 1.0
P A:A6 4.8 48.5 1.0
OP2 A:G42 4.9 62.0 1.0

Magnesium binding site 2 out of 5 in 4enc

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Magnesium binding site 2 out of 5 in the Crystal Structure of Fluoride Riboswitch


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:57.7
occ:1.00
O A:HOH210 2.0 50.5 1.0
O A:HOH201 2.1 60.5 1.0
OP2 A:A40 2.1 69.6 1.0
O A:HOH209 2.1 46.1 1.0
O A:HOH211 2.1 53.5 1.0
P A:A40 3.2 59.4 1.0
O5' A:A40 3.3 53.4 1.0
O4 A:U7 4.0 47.0 1.0
C3' A:G39 4.1 56.1 1.0
O3' A:G39 4.2 61.2 1.0
OP1 A:A40 4.4 64.5 1.0
O5' A:G39 4.5 63.6 1.0
O2 A:C50 4.6 74.1 1.0
N1 A:A49 4.6 56.1 1.0
C5' A:A40 4.7 46.2 1.0
N3 A:C50 4.8 66.1 1.0
O4' A:A40 4.8 45.8 1.0
OP2 A:G39 4.8 65.7 1.0
C2' A:G39 5.0 59.0 1.0
C8 A:G39 5.0 50.0 1.0

Magnesium binding site 3 out of 5 in 4enc

Go back to Magnesium Binding Sites List in 4enc
Magnesium binding site 3 out of 5 in the Crystal Structure of Fluoride Riboswitch


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:54.3
occ:1.00
F A:F106 1.9 37.5 1.0
OP2 A:A6 2.0 43.6 1.0
OP1 A:U41 2.0 44.0 1.0
OP2 A:G42 2.1 62.0 1.0
O A:HOH202 2.2 39.4 1.0
OP2 A:U7 2.2 39.3 1.0
P A:G42 3.0 52.7 1.0
MG A:MG104 3.2 38.1 1.0
OP1 A:G42 3.2 40.6 1.0
P A:A6 3.2 48.5 1.0
P A:U7 3.3 46.6 1.0
P A:U41 3.4 50.2 1.0
O A:HOH203 3.4 40.0 1.0
MG A:MG101 3.5 42.9 1.0
OP1 A:A6 3.6 48.0 1.0
OP1 A:U7 3.7 38.5 1.0
O5' A:U41 3.9 49.2 1.0
O3' A:A6 4.0 45.4 1.0
O3' A:U41 4.0 52.3 1.0
C5' A:U41 4.1 45.9 1.0
O A:HOH212 4.1 40.9 1.0
O3' A:G5 4.2 47.3 1.0
C3' A:A6 4.2 50.6 1.0
O5' A:G42 4.3 51.4 1.0
OP2 A:U41 4.3 42.0 1.0
O5' A:A6 4.3 45.6 1.0
O3' A:A40 4.4 49.3 1.0
O A:HOH204 4.4 36.6 1.0
O A:HOH208 4.5 42.2 1.0
C3' A:U41 4.5 46.9 1.0
O A:HOH205 4.6 41.2 1.0
C5' A:G42 4.6 58.8 1.0
N2 A:G39 4.6 38.9 1.0
O5' A:U7 4.6 53.3 1.0
C5' A:A6 4.8 56.6 1.0
C4' A:U41 4.9 50.2 1.0
K A:K107 5.0 75.4 1.0

Magnesium binding site 4 out of 5 in 4enc

Go back to Magnesium Binding Sites List in 4enc
Magnesium binding site 4 out of 5 in the Crystal Structure of Fluoride Riboswitch


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:38.1
occ:1.00
F A:F106 1.8 37.5 1.0
OP1 A:A6 2.0 48.0 1.0
OP1 A:G42 2.1 40.6 1.0
O A:HOH207 2.1 48.5 1.0
O A:HOH204 2.1 36.6 1.0
O A:HOH208 2.1 42.2 1.0
MG A:MG101 2.9 42.9 1.0
P A:A6 3.1 48.5 1.0
MG A:MG103 3.2 54.3 1.0
P A:G42 3.2 52.7 1.0
OP2 A:A6 3.3 43.6 1.0
O A:HOH205 3.5 41.2 1.0
K A:K107 3.5 75.4 1.0
OP1 A:U7 3.6 38.5 1.0
OP2 A:G42 3.7 62.0 1.0
O3' A:U41 3.8 52.3 1.0
O3' A:G5 3.9 47.3 1.0
C3' A:G5 4.3 44.7 1.0
OP2 A:U7 4.3 39.3 1.0
P A:U7 4.4 46.6 1.0
O5' A:A6 4.4 45.6 1.0
O A:HOH203 4.5 40.0 1.0
OP2 A:G5 4.5 55.8 1.0
O5' A:G42 4.6 51.4 1.0
OP1 A:U41 4.6 44.0 1.0
OP2 A:G8 4.6 53.6 1.0
O5' A:G5 4.6 58.9 1.0
O A:HOH206 4.8 46.6 1.0
OP1 A:G5 4.8 67.8 1.0
P A:G5 4.8 52.0 1.0
O3' A:A6 4.9 45.4 1.0
C5' A:U41 4.9 45.9 1.0
C3' A:U41 4.9 46.9 1.0

Magnesium binding site 5 out of 5 in 4enc

Go back to Magnesium Binding Sites List in 4enc
Magnesium binding site 5 out of 5 in the Crystal Structure of Fluoride Riboswitch


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:0.3
occ:1.00
O3' A:G52 2.2 98.6 1.0
O2' A:G52 2.6 0.0 1.0
C3' A:G52 2.6 0.7 1.0
C2' A:G52 3.1 0.1 1.0
C4' A:G52 4.1 0.8 1.0
C1' A:G52 4.4 0.4 1.0
O4' A:G52 4.9 98.0 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 Dec 14 14:14:16 2020

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