Magnesium in PDB 6dn3: Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna

The structure of Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna, PDB code: 6dn3 was solved by Q.Vicens, E.Mondragon, F.E.Reyes, J.Berman, H.Kaur, K.Kells, P.Wickens, J.Wilson, R.Gadwood, H.Schostarez, R.K.Suto, P.Coish, K.F.Blount, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.10 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.550, 71.550, 140.270, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 22.9

The structure of Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna (pdb code 6dn3). 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 the Fmn Riboswitch Bound to BRX1555 Split Rna, PDB code: 6dn3:
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 the Fmn Riboswitch Bound to BRX1555 Split Rna


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 BRX1555 Split Rna within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg102 b:51.0 occ:1.00 OP1 X:G16 4.0 73.1 1.0 OP1 X:G15 4.3 66.0 1.0 OP2 X:G16 4.5 72.6 1.0 P X:G16 4.6 72.5 1.0 O3' X:G15 4.9 70.4 1.0 C5' X:G15 4.9 67.2 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna


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 BRX1555 Split Rna within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg103 b:73.0 occ:1.00 N3 X:A14 3.8 70.3 1.0 O2' X:A29 4.2 62.8 1.0 C2 X:A14 4.4 70.5 1.0 C4 X:A14 4.5 69.8 1.0 C1' X:A14 4.5 70.8 1.0 N9 X:A14 4.8 70.3 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna


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 BRX1555 Split Rna within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg104 b:75.1 occ:1.00 O4 X:U37 3.6 70.9 1.0 OP2 X:A40 3.7 55.6 1.0 O6 X:G36 4.0 66.2 1.0 N7 X:G36 4.2 68.8 1.0 O2' X:A40 4.3 56.7 1.0 C2' X:A40 4.4 55.7 1.0 O6 X:G35 4.5 70.6 1.0 N7 X:G35 4.7 72.2 1.0 C4 X:U37 4.7 71.2 1.0 P X:A40 4.8 56.2 1.0 C6 X:G36 4.8 67.0 1.0 O5' X:A40 4.9 56.6 1.0 C5 X:G36 4.9 67.9 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna


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 BRX1555 Split Rna within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg105 b:73.9 occ:1.00 OP2 X:A49 2.5 70.3 1.0 N7 X:A50 3.9 74.7 1.0 P X:A49 3.9 70.4 1.0 N7 X:A49 4.1 62.0 1.0 C8 X:A49 4.4 62.9 1.0 O5' X:A49 4.4 69.1 1.0 OP2 X:A48 4.5 74.0 1.0 O5' X:A48 4.6 72.4 1.0 OP1 X:A48 4.6 74.5 1.0 N6 X:A50 4.7 73.8 1.0 OP1 X:A49 4.7 70.6 1.0 C8 X:A50 4.8 75.8 1.0 P X:A48 4.8 74.0 1.0 C5 X:A50 4.9 74.2 1.0 O3' X:A48 5.0 69.8 1.0 C5 X:A49 5.0 60.6 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna


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 BRX1555 Split Rna within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg203 b:53.2 occ:1.00 OP2 Y:G62 4.1 75.9 1.0 N6 Y:A63 4.2 61.0 1.0 N7 Y:A63 4.7 60.9 1.0 OP2 X:C43 4.7 61.6 1.0 N7 Y:G62 4.8 56.4 1.0 N4 X:C46 4.8 76.6 1.0 OP1 X:C43 4.9 63.5 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna


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 BRX1555 Split Rna within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg204 b:58.9 occ:1.00 O6 Y:G84 4.1 51.7 1.0 OP2 Y:C83 4.4 64.9 1.0 N7 Y:G84 4.4 52.0 1.0 C5 Y:C83 4.4 56.5 1.0 O6 Y:G93 4.5 47.3 1.0 N4 Y:C83 4.9 54.7 1.0 N4 X:C30 4.9 47.0 1.0 C4 Y:C83 4.9 55.1 1.0 C6 Y:G84 5.0 51.6 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to BRX1555 Split Rna


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 BRX1555 Split Rna within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg205 b:55.2 occ:1.00 OP2 Y:A92 2.1 66.7 1.0 O4 Y:U89 2.5 89.8 1.0 P Y:A92 3.5 67.0 1.0 C4 Y:U89 3.6 90.2 1.0 N7 Y:G88 4.1 88.1 1.0 C5 Y:U89 4.3 90.8 1.0 O3' Y:G91 4.3 68.6 1.0 OP1 Y:A92 4.3 67.1 1.0 O5' Y:A92 4.5 64.9 1.0 C5' Y:G91 4.6 74.8 1.0 C4' Y:G91 4.6 72.3 1.0 C3' Y:G91 4.6 70.4 1.0 O6 Y:G88 4.7 86.3 1.0 N3 Y:U89 4.8 90.1 1.0 C8 Y:A92 4.8 58.1 1.0 C8 Y:G88 4.9 88.4 1.0

Q.Vicens, E.Mondragon, F.E.Reyes, P.Coish, P.Aristoff, J.Berman, H.Kaur, K.W.Kells, P.Wickens, J.Wilson, R.C.Gadwood, H.J.Schostarez, R.K.Suto, K.F.Blount, R.T.Batey. Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch. Acs Chem. Biol. V. 13 2908 2018.
ISSN: ESSN 1554-8937
PubMed: 30107111
DOI: 10.1021/ACSCHEMBIO.8B00533