Magnesium in PDB 8uta: Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N

The structure of Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N, PDB code: 8uta was solved by D.Krochmal, A.Lewicka, J.A.Piccirilli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.79 / 3.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.873, 75.138, 95.727, 87.25, 87.99, 87.72
R / Rfree (%)	22.4 / 26.9

The binding sites of Magnesium atom in the Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N (pdb code 8uta). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N, PDB code: 8uta:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg201 b:49.7 occ:1.00 OP1 N:C59 2.6 165.5 1.0 OP2 N:U96 2.6 128.3 1.0 OP2 N:A94 3.6 129.0 1.0 P N:U96 3.7 136.0 1.0 P N:C59 3.9 141.6 1.0 OP1 N:U96 4.0 131.8 1.0 O3' N:G95 4.3 128.3 1.0 P N:A94 4.4 129.3 1.0 OP1 N:A94 4.5 128.8 1.0 O3' N:U58 4.5 140.8 1.0 OP2 N:C60 4.6 144.0 1.0 OP2 N:C59 4.7 141.6 1.0 OP1 N:A93 4.7 157.4 1.0 O3' N:A93 4.8 129.7 1.0

Magnesium binding site 2 out of 6 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg202 b:81.2 occ:1.00 N7 N:G57 3.1 148.1 1.0 O4 N:U58 3.5 138.3 1.0 O6 N:G57 3.6 152.4 1.0 C5 N:G57 3.6 139.4 1.0 C6 N:G57 3.8 142.2 1.0 C8 N:G57 4.0 143.6 1.0 C5 N:U58 4.0 139.1 1.0 C4 N:U58 4.1 138.5 1.0 OP1 N:G57 4.6 156.4 1.0 C4 N:G57 4.7 139.7 1.0 OP2 N:A15 4.7 151.2 1.0 N9 N:G57 4.8 140.3 1.0

Magnesium binding site 3 out of 6 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg203 b:64.9 occ:1.00 O6 N:G50 2.9 171.9 1.0 N7 N:G49 3.0 145.4 1.0 O6 N:G49 3.4 172.7 1.0 C5 N:G49 3.6 151.5 1.0 C6 N:G49 3.7 161.5 1.0 C6 N:G50 3.8 177.7 1.0 N7 N:G50 4.0 173.2 1.0 C8 N:G49 4.0 143.2 1.0 N4 N:C59 4.2 183.0 1.0 C5 N:G50 4.3 171.8 1.0 N4 N:C48 4.3 151.2 1.0 C4 N:C48 4.3 152.7 1.0 C5 N:C48 4.4 145.3 1.0 C4 N:G49 4.8 148.1 1.0 O2' N:A56 4.8 143.1 1.0 N3 N:C48 4.9 154.3 1.0 O4 N:U51 4.9 147.8 1.0 N9 N:G49 4.9 130.0 1.0 N1 N:G49 5.0 174.7 1.0

Magnesium binding site 4 out of 6 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg201 b:62.4 occ:1.00 OP1 R:C59 2.7 150.4 1.0 OP2 R:U96 2.7 183.7 1.0 OP2 R:A94 2.9 183.1 1.0 P R:U96 3.4 183.9 1.0 OP1 R:A94 3.5 184.2 1.0 OP1 R:U96 3.5 184.4 1.0 P R:A94 3.6 183.6 1.0 O3' R:G95 3.7 183.4 1.0 P R:C59 4.1 131.5 1.0 C3' R:G95 4.2 183.5 1.0 O2' R:G95 4.4 182.6 1.0 O3' R:A93 4.4 183.6 1.0 C5' R:A93 4.6 182.6 1.0 O3' R:U58 4.8 131.4 1.0 C2' R:G95 4.9 183.1 1.0 O5' R:U96 4.9 184.1 1.0 OP2 R:C60 4.9 135.2 1.0 OP2 R:C59 5.0 130.8 1.0 O5' R:A94 5.0 183.7 1.0

Magnesium binding site 5 out of 6 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg202 b:85.8 occ:1.00 N7 R:G57 2.9 156.7 1.0 O6 R:G57 3.8 186.5 1.0 C8 R:G57 3.9 137.4 1.0 C5 R:G57 3.9 165.2 1.0 C6 R:G57 4.2 181.8 1.0 OP1 R:G57 4.5 161.7 1.0 O4 R:U58 4.9 172.5 1.0

Magnesium binding site 6 out of 6 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yjdf Riboswitch From R. Gauvreauii in Complex with Proflavine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg203 b:67.2 occ:1.00 N7 R:G62 3.8 131.4 1.0 O6 R:G62 4.1 131.9 1.0 N7 R:G61 4.6 132.7 1.0 C5 R:G62 4.6 133.5 1.0 C6 R:G62 4.7 131.5 1.0 O6 R:G61 4.7 130.5 1.0 C8 R:G62 4.8 138.6 1.0

D.Krochmal, C.Roman, A.Lewicka, Y.Shao, J.A.Piccirilli. Structural Basis For Promiscuity in Ligand Recognition By Yjdf Riboswitch Cell Discov V. 10 37 2024.
ISSN: ESSN 2056-5968
DOI: 10.1038/S41421-024-00663-2