Magnesium in PDB 2yif: Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State

The structure of Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State, PDB code: 2yif 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)	29.844 / 3.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	73.472, 73.472, 135.168, 90.00, 90.00, 120.00
R / Rfree (%)	20.58 / 25.72

The structure of Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State also contains other interesting chemical elements:

Potassium

(K)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State (pdb code 2yif). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State, PDB code: 2yif:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1054 b:1.0 occ:1.00 O X:HOH2004 1.8 1.0 1.0 O X:HOH2006 1.8 1.0 1.0 O X:HOH2005 1.8 1.0 1.0 O X:HOH2003 1.8 1.0 1.0 O X:HOH2007 1.9 1.0 1.0 OP2 X:A14 2.6 85.7 1.0 N7 X:G15 4.0 92.5 1.0 P X:A14 4.0 0.0 1.0 OP2 X:G15 4.4 88.7 1.0 N7 X:G16 4.5 95.3 1.0 O5' X:A14 4.5 1.0 1.0 C8 X:G15 4.6 93.5 1.0 O2' X:C13 4.8 84.2 1.0 O4' X:U23 4.8 93.3 1.0 O3' X:C13 4.8 80.3 1.0 C2' X:C13 5.0 79.2 1.0 C5 X:G15 5.0 96.4 1.0

Magnesium binding site 2 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1055 b:87.2 occ:1.00 O6 X:G28 2.6 0.7 1.0 C6 X:G28 3.8 0.8 1.0 OP1 X:C25 4.0 0.6 1.0 N6 X:A29 4.2 0.6 1.0 C5 X:G28 4.8 99.5 1.0 N1 X:G28 4.8 99.0 1.0 O4 Z:U94 4.9 85.1 1.0 OP2 X:C26 4.9 0.4 1.0 N7 X:G28 4.9 0.2 1.0

Magnesium binding site 3 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1057 b:68.3 occ:1.00 OP1 X:G16 3.6 92.2 1.0 OP1 X:G15 4.4 90.1 1.0 P X:G16 4.6 89.6 1.0 OP2 X:G16 4.8 89.7 1.0

Magnesium binding site 4 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1058 b:93.4 occ:1.00 N7 X:G19 4.2 0.2 1.0 O6 X:G19 4.3 0.3 1.0 OP1 X:A21 4.4 0.7 1.0 C5 X:G19 4.8 1.0 1.0 C6 X:G19 4.8 0.9 1.0

Magnesium binding site 5 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg1059 b:78.2 occ:1.00 N3 X:A14 4.0 0.1 1.0 O2' X:A29 4.1 0.3 1.0 C2 X:A14 4.5 0.6 1.0 C4 X:A14 4.5 0.7 1.0 C1' X:A14 4.7 0.3 1.0 N9 X:A14 4.8 0.7 1.0

Magnesium binding site 6 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg1114 b:87.7 occ:1.00 N7 Z:G84 3.7 95.5 1.0 OP1 Z:G93 3.9 97.2 1.0 N7 Z:G93 3.9 88.5 1.0 C8 Z:G93 4.2 87.2 1.0 C8 Z:G84 4.2 95.3 1.0 OP1 Z:G84 4.5 0.7 1.0 P Z:G93 4.8 0.3 1.0 C5 Z:G84 4.8 91.8 1.0 O5' Z:G93 5.0 0.0 1.0

Magnesium binding site 7 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg1115 b:0.7 occ:1.00 O Z:HOH2006 1.8 0.7 1.0 O Z:HOH2011 1.9 0.7 1.0 O Z:HOH2012 1.9 0.7 1.0 O Z:HOH2007 1.9 0.7 1.0 OP1 Z:A92 2.4 95.5 1.0 O4 Z:U89 2.6 90.4 1.0 C4 Z:U89 3.8 94.5 1.0 P Z:A92 3.9 89.7 1.0 N7 Z:G88 4.3 0.6 1.0 O6 Z:G88 4.5 0.6 1.0 C8 Z:A92 4.6 99.7 1.0 OP2 Z:A92 4.6 89.0 1.0 O5' Z:A92 4.6 88.4 1.0 N3 Z:U89 4.6 93.9 1.0 C5 Z:U89 4.7 0.1 1.0 O3' Z:G91 4.9 83.4 1.0

Magnesium binding site 8 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg1116 b:1.0 occ:1.00 O X:HOH2001 1.8 1.0 1.0 O X:HOH2002 1.8 1.0 1.0 O Z:HOH2014 1.8 1.0 1.0 O Z:HOH2015 1.8 1.0 1.0 O Z:HOH2013 1.8 1.0 1.0 OP1 Z:C95 3.0 99.6 1.0 N7 X:G12 3.5 0.5 1.0 OP2 Z:C95 3.8 99.8 1.0 P Z:C95 3.9 0.4 1.0 OP2 X:G12 4.1 0.6 1.0 C8 X:G12 4.3 0.9 1.0 O6 X:G12 4.6 0.7 1.0 C5 X:G12 4.6 0.7 1.0 O3' Z:U94 4.7 0.2 1.0 C6 X:G12 5.0 98.7 1.0

Magnesium binding site 9 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg1117 b:65.7 occ:1.00 O6 Z:G67 3.7 0.0 1.0 O6 Z:G68 3.7 0.2 1.0 OP1 Z:U75 3.9 0.5 1.0 O4 Z:U66 4.3 88.1 1.0 N4 Z:C76 4.4 93.8 1.0 C6 Z:G67 4.5 0.8 1.0 C5 Z:U66 4.7 0.1 1.0 N7 Z:G67 4.7 0.3 1.0 C4 Z:U66 4.8 97.1 1.0 C4' Z:U74 4.8 0.6 1.0 P Z:U75 4.8 85.0 1.0 C6 Z:G68 4.9 0.1 1.0 O2' Z:A73 4.9 0.1 1.0 C5 Z:G67 5.0 0.2 1.0 OP2 Z:U75 5.0 99.9 1.0

Magnesium binding site 10 out of 12 in the Crystal Structure of A F. Nucleatum Fmn Riboswitch - Free State


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 - Free State within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg1118 b:51.5 occ:1.00 O6 Z:G91 3.9 0.3 1.0 N1 Z:A90 4.1 0.5 1.0 N6 X:A22 4.2 0.8 1.0 C2 Z:A90 4.2 0.0 1.0 C6 Z:G91 5.0 99.8 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