Manganese 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:

Magnesium	(Mg)	11 atoms
Potassium	(K)	2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak., PDB code: 3f2y:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn401 b:0.3 occ:0.50 N7 X:G19 3.6 0.5 1.0 C8 X:G19 4.2 0.6 1.0 OP2 X:G19 4.3 0.6 1.0 C5 X:G19 4.7 0.5 1.0 OP2 X:U18 4.8 0.3 1.0 O6 X:G19 5.0 0.8 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn402 b:0.2 occ:1.00 N7 X:G93 2.6 95.6 1.0 C8 X:G93 3.4 95.4 1.0 C5 X:G93 3.8 95.5 1.0 O6 X:G93 4.1 95.2 1.0 OP1 X:G93 4.1 94.7 1.0 O4 X:U94 4.3 90.5 1.0 C6 X:G93 4.3 95.6 1.0 N7 X:G84 4.5 93.2 1.0 N9 X:G93 4.7 94.9 1.0 C4 X:G93 4.9 95.3 1.0 MG X:MG310 5.0 0.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn403 b:0.9 occ:1.00 OP2 X:A92 2.1 88.7 1.0 O4 X:U89 2.1 0.6 1.0 C4 X:U89 3.3 0.6 1.0 P X:A92 3.5 89.2 1.0 C5 X:U89 4.0 0.1 1.0 N7 X:G88 4.0 1.0 1.0 O6 X:G88 4.2 0.4 1.0 OP1 X:A92 4.2 89.1 1.0 O5' X:A92 4.3 90.1 1.0 N3 X:U89 4.4 0.7 1.0 O3' X:G91 4.5 88.0 1.0 C5' X:G91 4.6 88.9 1.0 C8 X:A92 4.7 92.6 1.0 C3' X:G91 4.7 87.0 1.0 C4' X:G91 4.7 87.2 1.0 C5 X:G88 4.8 0.8 1.0 C6 X:G88 4.8 0.0 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn404 b:85.2 occ:1.00 N7 X:G33 2.3 0.4 1.0 O1P X:FMN200 2.4 78.1 1.0 C8 X:G33 3.2 0.5 1.0 O3P X:FMN200 3.3 78.3 1.0 C5 X:G33 3.4 0.3 1.0 P X:FMN200 3.4 78.1 1.0 O6 X:G33 3.6 0.7 1.0 O2' X:G41 3.9 99.2 1.0 C6 X:G33 3.9 0.4 1.0 O4' X:G41 4.2 99.4 1.0 OP2 X:G33 4.3 0.0 1.0 O6 X:G62 4.3 0.5 1.0 N1 X:G10 4.3 0.5 1.0 N2 X:G10 4.3 0.5 1.0 C4' X:G41 4.3 99.3 1.0 O5' X:FMN200 4.4 79.5 1.0 N9 X:G33 4.5 0.5 1.0 O2P X:FMN200 4.6 79.0 1.0 C4 X:G33 4.6 0.2 1.0 N1 X:G62 4.7 0.1 1.0 C1' X:G41 4.7 99.2 1.0 C2 X:G10 4.8 0.4 1.0 C2' X:G41 4.8 99.2 1.0 C6 X:G62 5.0 0.2 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