Magnesium in PDB 3f2y: Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak., PDB code: 3f2y was solved by A.A.Serganov, L.Huang, 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 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.988, 70.988, 140.004, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 23.7

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak. also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Manganese	(Mn)	4 atoms

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak. (pdb code 3f2y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak., PDB code: 3f2y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg306 b:83.0 occ:1.00 OP2 X:A14 2.0 0.4 1.0 O2' X:C13 3.4 0.2 1.0 P X:A14 3.4 0.8 1.0 N7 X:G15 3.5 0.1 1.0 O6 X:G15 3.8 0.6 1.0 C2' X:C13 3.9 0.5 1.0 O3' X:C13 4.1 0.3 1.0 O5' X:A14 4.3 0.8 1.0 C5 X:G15 4.3 0.1 1.0 C6 X:G15 4.4 0.3 1.0 C3' X:C13 4.4 1.0 1.0 N7 X:G16 4.4 0.8 1.0 OP1 X:A14 4.4 0.7 1.0 O4' X:U23 4.5 99.4 1.0 C8 X:G15 4.6 0.1 1.0 OP2 X:G15 4.7 0.7 1.0

Magnesium binding site 2 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg307 b:86.6 occ:1.00 OP2 X:G16 4.3 0.4 1.0 OP1 X:G16 4.4 0.3 1.0 OP1 X:G15 4.6 0.2 1.0 P X:G16 4.8 0.4 1.0

Magnesium binding site 3 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg308 b:0.2 occ:1.00 O2B X:GTP1 1.9 0.5 1.0 OP2 X:G2 2.5 0.3 1.0 PB X:GTP1 3.1 0.5 1.0 O1B X:GTP1 3.4 0.5 1.0 O3B X:GTP1 3.7 0.8 1.0 P X:G2 3.9 0.3 1.0 N7 X:G2 4.2 0.4 1.0 O5' X:G2 4.4 0.6 1.0 O3A X:GTP1 4.4 0.5 1.0 C8 X:G2 4.5 0.5 1.0 O5' X:GTP1 4.6 0.5 1.0 OP1 X:G2 4.8 0.4 1.0 C3' X:GTP1 4.9 0.8 1.0 O3' X:GTP1 5.0 0.4 1.0

Magnesium binding site 4 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg309 b:97.7 occ:1.00 O6 X:G68 3.9 0.2 1.0 C4' X:U74 4.0 95.7 1.0 OP2 X:U75 4.2 92.3 1.0 O6 X:G67 4.2 0.3 1.0 C5' X:U74 4.4 95.9 1.0 O4' X:U74 4.6 96.1 1.0 O3' X:U74 4.7 94.1 1.0 N7 X:G67 4.8 0.9 1.0 O4 X:U66 4.9 0.2 1.0 O5' X:U74 4.9 96.5 1.0 N4 X:C76 4.9 94.2 1.0 C3' X:U74 4.9 95.3 1.0 P X:U75 5.0 92.5 1.0

Magnesium binding site 5 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg310 b:0.4 occ:1.00 O6 X:G28 2.4 0.1 1.0 C6 X:G28 3.7 0.4 1.0 N6 X:A29 4.1 0.7 1.0 O4 X:U94 4.3 90.5 1.0 N3 X:C13 4.4 0.0 1.0 OP2 X:C25 4.4 0.5 1.0 N1 X:G28 4.5 0.1 1.0 C5 X:G28 4.8 0.3 1.0 O2 X:C13 4.9 0.4 1.0 MN X:MN402 5.0 0.2 1.0 N4 X:C13 5.0 0.6 1.0

Magnesium binding site 6 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg311 b:87.9 occ:1.00 O6 X:G32 4.0 0.4 1.0 O6 X:G41 4.1 98.8 1.0 N7 X:G32 4.2 0.5 1.0 C6 X:G32 4.8 0.4 1.0 N4 X:C82 4.9 97.8 1.0 C5 X:G32 4.9 0.9 1.0 C5 X:C31 4.9 0.0 1.0 N4 X:C31 4.9 0.2 1.0 C6 X:G41 5.0 98.7 1.0

Magnesium binding site 7 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg313 b:0.8 occ:1.00 N3 X:A14 4.3 0.9 1.0 O2' X:A29 4.4 0.1 1.0 C1' X:A14 4.7 0.6 1.0 O3' X:A29 4.8 0.9 1.0 C4 X:A14 4.8 0.5 1.0 N9 X:A14 4.9 0.0 1.0 C2 X:A14 4.9 0.8 1.0

Magnesium binding site 8 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg314 b:0.0 occ:1.00 OP2 X:U23 2.0 0.6 1.0 OP1 X:A22 2.3 0.5 1.0 P X:U23 3.3 0.7 1.0 P X:A22 3.7 0.7 1.0 OP1 X:U23 3.8 0.7 1.0 O5' X:U23 4.1 0.8 1.0 O5' X:A22 4.4 0.6 1.0 OP2 X:A22 4.4 0.7 1.0 C5' X:A22 4.4 0.9 1.0 O3' X:A22 4.5 0.8 1.0 C5' X:U23 4.6 0.0 1.0 C3' X:A22 4.6 0.1 1.0 O3' X:A21 4.7 0.9 1.0

Magnesium binding site 9 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg315 b:0.8 occ:1.00 OP2 X:U65 3.0 0.5 1.0 N3 X:U74 3.1 97.4 1.0 O4 X:U74 3.4 97.5 1.0 C5' X:C43 3.6 0.9 1.0 C4 X:U74 3.6 97.6 1.0 C2 X:U74 4.0 97.3 1.0 O5' X:C43 4.2 0.6 1.0 O2 X:U74 4.2 97.5 1.0 P X:U65 4.3 0.4 1.0 C4' X:C43 4.3 0.7 1.0 C3' X:U64 4.6 0.5 1.0 OP1 X:U65 4.8 0.5 1.0 C5 X:U74 4.9 97.5 1.0 O3' X:U64 4.9 0.5 1.0 O2' X:U42 4.9 0.5 1.0

Magnesium binding site 10 out of 11 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


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 the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg316 b:0.3 occ:1.00 OP2 X:U6 4.6 0.9 1.0

A.Serganov, L.Huang, D.J.Patel. Coenzyme Recognition and Gene Regulation By A Flavin Mononucleotide Riboswitch. Nature V. 458 233 2009.
ISSN: ISSN 0028-0836
PubMed: 19169240
DOI: 10.1038/NATURE07642