Magnesium in PDB 2yie: Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn

The structure of Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn, PDB code: 2yie was solved by Q.Vicens, E.Mondragon, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.292 / 2.94
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	73.679, 73.679, 139.251, 90.00, 90.00, 120.00
R / Rfree (%)	20.41 / 23.14

The structure of Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn also contains other interesting chemical elements:

Potassium

(K)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn (pdb code 2yie). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn, PDB code: 2yie:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1055 b:79.5 occ:1.00 O X:HOH2011 1.9 79.5 1.0 O X:HOH2012 1.9 79.5 1.0 O X:HOH2014 1.9 79.5 1.0 O X:HOH2013 1.9 79.5 1.0 O2P Z:FMN1114 2.4 59.4 1.0 N7 X:G33 2.5 69.8 1.0 C8 X:G33 3.3 67.6 1.0 O1P Z:FMN1114 3.4 59.1 1.0 P Z:FMN1114 3.4 56.5 1.0 C5 X:G33 3.7 72.3 1.0 O6 X:G33 3.9 78.0 1.0 N1 X:G10 4.1 68.6 1.0 C6 X:G33 4.2 75.8 1.0 O2' X:G41 4.2 68.0 1.0 O5' Z:FMN1114 4.2 60.5 1.0 O6 Z:G62 4.2 71.6 1.0 N2 X:G10 4.5 70.2 1.0 O4' X:G41 4.5 61.3 1.0 C4' X:G41 4.6 64.9 1.0 N1 Z:G62 4.6 71.0 1.0 N9 X:G33 4.6 69.0 1.0 O3P Z:FMN1114 4.6 58.6 1.0 O6 X:G10 4.8 70.5 1.0 C4 X:G33 4.8 71.9 1.0 C2 X:G10 4.8 69.5 1.0 C1' X:G41 4.8 62.3 1.0 OP1 X:G33 4.9 62.9 1.0 C6 Z:G62 4.9 72.1 1.0 C6 X:G10 4.9 69.4 1.0

Magnesium binding site 2 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1056 b:79.0 occ:1.00 O X:HOH2005 2.8 61.1 1.0 O6 X:G28 3.2 67.3 1.0 N3 X:C13 3.5 74.1 1.0 OP1 X:C25 3.8 79.5 1.0 O4 Z:U94 3.9 70.1 1.0 N4 X:C13 3.9 72.8 1.0 N6 X:A29 4.1 66.3 1.0 C4 X:C13 4.1 72.2 1.0 OP2 X:U24 4.3 80.1 1.0 C2 X:C13 4.4 71.7 1.0 C6 X:G28 4.4 69.0 1.0 O2 X:C13 4.4 73.3 1.0 C4 Z:U94 4.7 66.5 1.0 N1 X:G28 4.9 66.5 1.0 C6 X:A29 4.9 71.2 1.0

Magnesium binding site 3 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1057 b:69.0 occ:1.00 O6 X:G32 3.9 50.8 1.0 O6 X:G41 4.0 63.6 1.0 N7 X:G32 4.3 64.5 1.0 C6 X:G32 4.7 49.6 1.0 N4 X:C31 4.7 56.6 1.0 C5 X:C31 4.8 70.1 1.0 C5 X:G32 4.9 55.4 1.0 N4 Z:C82 4.9 67.3 1.0 C6 X:G41 4.9 64.1 1.0

Magnesium binding site 4 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1058 b:80.9 occ:1.00 OP2 X:U23 2.8 86.9 1.0 O X:HOH2004 3.1 55.4 1.0 OP1 X:A22 3.2 0.6 1.0 C5' X:U23 3.9 82.0 1.0 P X:A22 3.9 0.5 1.0 OP2 X:A22 3.9 0.9 1.0 P X:U23 4.1 84.9 1.0 O5' X:U23 4.2 84.4 1.0 O5' X:A22 4.3 95.9 1.0 C3' X:A22 4.9 83.7 1.0 O3' X:A22 4.9 85.9 1.0

Magnesium binding site 5 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1059 b:87.3 occ:1.00 O X:HOH2025 1.8 87.3 1.0 O X:HOH2022 1.8 87.3 1.0 O X:HOH2021 1.8 87.3 1.0 O X:HOH2024 1.8 87.3 1.0 O X:HOH2023 1.9 87.3 1.0 OP2 X:A14 2.2 69.3 1.0 P X:A14 3.6 76.0 1.0 O4' X:U23 4.3 74.9 1.0 O5' X:A14 4.3 76.8 1.0 N7 X:G15 4.4 70.4 1.0 OP1 X:A14 4.5 63.7 1.0 O2' X:C13 4.5 70.5 1.0 O3' X:C13 4.6 71.4 1.0 OP2 X:G15 4.6 68.1 1.0 N7 X:G16 4.6 73.7 1.0 C2' X:C13 4.8 69.6 1.0 C4' X:U23 4.9 78.0 1.0

Magnesium binding site 6 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1060 b:92.8 occ:1.00 O X:HOH2003 2.7 64.7 1.0 O X:HOH2002 2.8 77.9 1.0 N7 X:G19 4.0 89.6 1.0 OP1 X:U18 4.7 88.5 1.0 O6 X:G19 4.7 74.1 1.0 C8 X:G19 4.9 94.5 1.0 C5 X:G19 4.9 82.1 1.0

Magnesium binding site 7 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1061 b:76.4 occ:1.00 OP1 X:G15 4.3 66.2 1.0 OP1 X:G16 4.3 80.0 1.0 OP2 X:G16 4.7 75.4 1.0 P X:G16 4.9 69.2 1.0 O3' X:G15 5.0 80.2 1.0

Magnesium binding site 8 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1062 b:64.2 occ:1.00 N3 X:A14 4.5 62.7 1.0 O2' X:A29 4.7 70.6 1.0 O3' X:A29 4.7 70.5 1.0 C2 X:A14 5.0 64.0 1.0

Magnesium binding site 9 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg1115 b:75.3 occ:1.00 N7 Z:G93 3.0 71.6 1.0 C8 Z:G93 3.8 68.1 1.0 C5 Z:G93 4.1 71.5 1.0 O6 Z:G93 4.1 81.2 1.0 OP1 Z:G93 4.4 68.0 1.0 C6 Z:G93 4.5 76.8 1.0 N7 Z:G84 4.8 63.2 1.0 O4 Z:U94 4.8 70.1 1.0

Magnesium binding site 10 out of 14 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch Bound to Fmn


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 A F. Nucleatum Fmn Riboswitch Bound to Fmn within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg1116 b:0.3 occ:1.00 O Z:HOH2011 1.9 0.3 1.0 O Z:HOH2012 1.9 0.3 1.0 O Z:HOH2014 1.9 0.3 1.0 O Z:HOH2013 1.9 0.3 1.0 OP1 Z:A92 2.3 66.3 1.0 O4 Z:U89 2.5 81.3 1.0 C4 Z:U89 3.7 83.3 1.0 P Z:A92 3.8 65.6 1.0 N7 Z:G88 4.0 69.7 1.0 O6 Z:G88 4.3 60.2 1.0 C5 Z:U89 4.4 87.6 1.0 O5' Z:A92 4.5 64.2 1.0 OP2 Z:A92 4.5 64.7 1.0 O3' Z:G91 4.7 80.1 1.0 N3 Z:U89 4.8 81.9 1.0 C5 Z:G88 4.8 66.9 1.0 C3' Z:G91 4.9 81.8 1.0 C6 Z:G88 4.9 62.4 1.0 C8 Z:A92 4.9 63.4 1.0 C8 Z:G88 5.0 75.0 1.0 C5' Z:G91 5.0 93.0 1.0 C4' Z:G91 5.0 85.4 1.0

Q.Vicens, E.Mondragon, R.T.Batey. Molecular Sensing By the Aptamer Domain of the Fmn Riboswitch: A General Model For Ligand Binding By Conformational Selection Nucleic Acids Res. V. 39 8586 2011.
ISSN: ISSN 0305-1048
PubMed: 21745821
DOI: 10.1093/NAR/GKR565