Magnesium in PDB 4enb: Crystal Structure of Fluoride Riboswitch, Bound to Iridium

The structure of Crystal Structure of Fluoride Riboswitch, Bound to Iridium, PDB code: 4enb 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)	46.19 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.949, 76.466, 42.824, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 25.3

The structure of Crystal Structure of Fluoride Riboswitch, Bound to Iridium also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Potassium	(K)	1 atom
Iridium	(Ir)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Fluoride Riboswitch, Bound to Iridium (pdb code 4enb). 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, Bound to Iridium, PDB code: 4enb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Fluoride Riboswitch, Bound to Iridium


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, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:69.3 occ:1.00 N2 A:G2 3.3 55.4 1.0 N3 A:G2 3.5 59.6 1.0 O4' A:G3 3.5 52.8 1.0 N6 A:A19 3.7 70.9 1.0 C1' A:G3 3.8 52.6 1.0 C2 A:G2 3.9 53.4 1.0 O2' A:G2 3.9 57.2 1.0 N1 A:A20 4.0 60.4 1.0 C2' A:G2 4.3 59.8 1.0 C6 A:A19 4.4 70.3 1.0 C4' A:G3 4.4 54.2 1.0 O2' A:G3 4.6 50.0 1.0 O2 A:C18 4.6 65.3 1.0 N6 A:A20 4.6 60.0 1.0 C4 A:G2 4.7 57.6 1.0 N9 A:G3 4.7 51.1 1.0 C1' A:G2 4.8 58.0 1.0 C2 A:A20 4.8 61.8 1.0 C6 A:A20 4.8 59.6 1.0 C2' A:G3 4.9 49.4 1.0 C5 A:A19 4.9 64.3 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Fluoride Riboswitch, Bound to Iridium


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, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:73.5 occ:1.00 O2G A:GTP1 2.4 68.8 1.0 O1G A:GTP1 2.5 66.5 1.0 PG A:GTP1 3.0 68.8 0.0 O A:HOH216 3.0 60.7 1.0 O3G A:GTP1 3.7 74.4 1.0 O3B A:GTP1 4.4 74.5 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Fluoride Riboswitch, Bound to Iridium


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, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:86.7 occ:1.00 O A:HOH212 2.1 76.8 1.0 O A:HOH220 2.1 74.6 1.0 O A:HOH219 3.7 71.1 1.0 IR A:IRI103 4.0 71.5 0.2 O A:HOH217 4.3 62.4 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Fluoride Riboswitch, Bound to Iridium


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, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:32.1 occ:1.00 F A:F106 1.9 34.3 1.0 O A:HOH226 2.0 28.3 1.0 OP2 A:G8 2.0 31.2 1.0 O A:HOH232 2.0 34.2 1.0 O A:HOH235 2.1 30.9 1.0 OP1 A:U7 2.1 29.2 1.0 MG A:MG113 2.9 32.8 1.0 P A:U7 3.2 34.2 1.0 K A:K105 3.4 54.0 1.0 O A:HOH233 3.4 34.2 1.0 P A:G8 3.4 38.9 1.0 OP2 A:U7 3.5 36.9 1.0 MG A:MG112 3.6 37.4 1.0 OP1 A:A6 4.0 35.4 1.0 OP1 A:G8 4.1 38.1 1.0 O5' A:U7 4.1 36.6 1.0 O3' A:U7 4.1 35.3 1.0 OP1 A:U41 4.1 41.7 1.0 C3' A:U7 4.1 36.5 1.0 O A:HOH230 4.4 35.6 1.0 O A:HOH234 4.4 32.5 1.0 O2' A:A40 4.5 43.0 1.0 O3' A:A6 4.5 40.2 1.0 OP2 A:A6 4.5 36.1 1.0 O5' A:G8 4.5 41.3 1.0 OP1 A:G42 4.6 43.1 1.0 C5' A:U41 4.7 46.3 1.0 P A:A6 4.8 36.2 1.0 O3' A:A40 4.8 40.9 1.0 C5' A:U7 4.8 38.2 1.0 OP2 A:G42 4.8 43.7 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Fluoride Riboswitch, Bound to Iridium


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, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:49.6 occ:1.00 O A:HOH225 2.0 44.2 1.0 O A:HOH224 2.1 48.3 1.0 O A:HOH223 2.1 42.8 1.0 O A:HOH221 2.1 48.8 1.0 O A:HOH214 2.1 57.3 1.0 OP2 A:A40 2.4 46.0 1.0 P A:A40 3.5 48.3 1.0 O5' A:A40 3.6 46.9 1.0 O A:HOH229 3.9 45.5 1.0 O2 A:C50 4.1 56.9 1.0 O4 A:U7 4.3 42.8 1.0 N3 A:C50 4.4 53.0 1.0 C3' A:G39 4.5 49.6 1.0 N1 A:A49 4.5 45.7 1.0 O3' A:G39 4.5 48.8 1.0 OP1 A:A40 4.7 45.9 1.0 O5' A:G39 4.7 55.3 1.0 C2 A:C50 4.7 56.0 1.0 C5' A:A40 5.0 38.6 1.0 OP2 A:G39 5.0 52.8 1.0 N6 A:A49 5.0 50.0 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Fluoride Riboswitch, Bound to Iridium


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, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg112 b:37.4 occ:1.00 F A:F106 1.9 34.3 1.0 OP1 A:U41 1.9 41.7 1.0 OP2 A:U7 2.1 36.9 1.0 OP2 A:G42 2.1 43.7 1.0 OP2 A:A6 2.1 36.1 1.0 O A:HOH222 2.1 39.9 1.0 P A:G42 3.2 42.4 1.0 P A:U7 3.3 34.2 1.0 P A:A6 3.4 36.2 1.0 P A:U41 3.4 44.2 1.0 MG A:MG113 3.4 32.8 1.0 O A:HOH232 3.5 34.2 1.0 OP1 A:G42 3.5 43.1 1.0 MG A:MG110 3.6 32.1 1.0 OP1 A:U7 3.7 29.2 1.0 OP1 A:A6 3.8 35.4 1.0 O5' A:U41 3.9 42.8 1.0 O3' A:A6 4.1 40.2 1.0 C5' A:U41 4.1 46.3 1.0 O3' A:U41 4.1 48.2 1.0 O A:HOH227 4.2 40.1 1.0 C3' A:A6 4.3 39.4 1.0 O3' A:A40 4.3 40.9 1.0 O3' A:G5 4.4 42.8 1.0 OP2 A:U41 4.4 44.9 1.0 O5' A:G42 4.4 49.8 1.0 O5' A:A6 4.4 41.3 1.0 O5' A:U7 4.5 36.6 1.0 C3' A:U41 4.6 45.0 1.0 O A:HOH226 4.6 28.3 1.0 N2 A:G39 4.6 38.4 1.0 O A:HOH235 4.6 30.9 1.0 O A:HOH233 4.6 34.2 1.0 C5' A:G42 4.7 45.3 1.0 C5' A:A6 4.8 40.0 1.0 C4' A:U41 4.9 49.2 1.0 K A:K105 5.0 54.0 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Fluoride Riboswitch, Bound to Iridium


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, Bound to Iridium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg113 b:32.8 occ:1.00 F A:F106 1.9 34.3 1.0 OP1 A:A6 2.0 35.4 1.0 O A:HOH226 2.0 28.3 1.0 OP1 A:G42 2.0 43.1 1.0 O A:HOH234 2.1 32.5 1.0 O A:HOH233 2.1 34.2 1.0 MG A:MG110 2.9 32.1 1.0 P A:A6 3.0 36.2 1.0 P A:G42 3.1 42.4 1.0 OP2 A:A6 3.3 36.1 1.0 K A:K105 3.3 54.0 1.0 MG A:MG112 3.4 37.4 1.0 O A:HOH235 3.5 30.9 1.0 OP2 A:G42 3.6 43.7 1.0 OP1 A:U7 3.6 29.2 1.0 O3' A:U41 3.7 48.2 1.0 O3' A:G5 3.9 42.8 1.0 C3' A:G5 4.2 43.6 1.0 O5' A:A6 4.3 41.3 1.0 OP2 A:U7 4.3 36.9 1.0 P A:U7 4.4 34.2 1.0 O A:HOH232 4.5 34.2 1.0 O5' A:G42 4.5 49.8 1.0 O5' A:G5 4.6 40.4 1.0 OP2 A:G5 4.6 40.7 1.0 OP2 A:G8 4.7 31.2 1.0 OP1 A:G5 4.7 44.9 1.0 P A:G5 4.8 40.5 1.0 OP1 A:U41 4.8 41.7 1.0 O A:HOH230 4.9 35.6 1.0 C3' A:U41 4.9 45.0 1.0 O3' A:A6 5.0 40.2 1.0 C5' A:G5 5.0 38.7 1.0

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