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

The structure of Yjdf Riboswitch From R. Gauvreauii in Complex with Chelerythrine Bound to Fab BL3-6 S97N, PDB code: 8uiw 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)	95.70 / 2.77
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.792, 77.438, 95.848, 87.19, 88.43, 88.05
R / Rfree (%)	21.1 / 23.1

The structure of Yjdf Riboswitch From R. Gauvreauii in Complex with Chelerythrine Bound to Fab BL3-6 S97N also contains other interesting chemical elements:

Osmium	(Os)	4 atoms
Potassium	(K)	1 atom

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

Magnesium binding site 1 out of 5 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Chelerythrine 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 Chelerythrine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg201 b:109.2 occ:1.00 OP1 N:C59 2.3 99.1 1.0 OP2 N:U96 3.2 115.4 1.0 P N:C59 3.6 94.9 1.0 OP2 N:A94 3.7 117.7 1.0 OP2 N:C59 4.1 105.5 1.0 OP1 N:A93 4.1 130.2 1.0 O3' N:U58 4.2 102.0 1.0 P N:U96 4.4 112.5 1.0 P N:A94 4.4 135.8 1.0 OP1 N:A94 4.5 125.5 1.0 OP2 N:C60 4.7 95.0 1.0 O3' N:A93 4.7 129.2 1.0 OP1 N:U96 4.8 131.5 1.0 O5' N:C59 4.8 99.0 1.0 O3' N:G95 4.8 120.4 1.0

Magnesium binding site 2 out of 5 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Chelerythrine 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 Chelerythrine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg201 b:106.5 occ:1.00 OP1 R:C59 2.4 102.9 1.0 OP2 R:U96 2.9 114.8 1.0 OP2 R:A94 3.6 108.8 1.0 P R:U96 3.8 106.4 1.0 P R:C59 3.9 102.3 1.0 OP1 R:U96 4.0 108.0 1.0 O3' R:G95 4.1 112.0 1.0 OP1 R:A94 4.1 111.5 1.0 P R:A94 4.3 110.1 1.0 OP2 R:C60 4.5 109.3 1.0 O3' R:U58 4.7 102.4 1.0 OP2 R:C59 4.7 99.3 1.0 C3' R:G95 4.7 116.8 1.0 O5' R:C59 4.8 97.3 1.0 O2' R:G95 4.8 111.9 1.0 C5' R:C59 4.8 96.9 1.0

Magnesium binding site 3 out of 5 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Chelerythrine 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 Chelerythrine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg202 b:127.9 occ:1.00 OP1 R:A45 3.8 125.0 1.0 O2' R:C18 3.8 119.2 1.0 OP2 R:G44 4.0 152.4 1.0 OP1 R:G44 4.0 150.1 1.0 OP2 R:A93 4.2 106.3 1.0 N6 R:A19 4.4 124.0 1.0 P R:G44 4.4 129.6 1.0 N7 R:A19 4.4 123.3 1.0 N7 R:A93 4.4 112.6 1.0 O2 R:C18 4.5 115.2 1.0 N2 R:G57 4.5 119.3 1.0 O5' R:G44 4.5 123.0 1.0 C2' R:C18 4.7 123.0 1.0 C8 R:A93 4.8 107.0 1.0 N7 R:A45 4.8 115.8 1.0

Magnesium binding site 4 out of 5 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Chelerythrine 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 Chelerythrine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg203 b:123.3 occ:1.00 N7 R:G49 3.8 84.3 1.0 O2' R:A56 3.9 98.1 1.0 O6 R:G50 4.0 91.2 1.0 O6 R:G49 4.3 89.7 1.0 C2' R:A56 4.5 109.1 1.0 C5 R:G49 4.6 84.1 1.0 C8 R:G49 4.6 84.6 1.0 N7 R:G50 4.7 87.1 1.0 C6 R:G49 4.8 87.4 1.0 C6 R:G50 4.9 87.3 1.0

Magnesium binding site 5 out of 5 in the Yjdf Riboswitch From R. Gauvreauii in Complex with Chelerythrine 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 Chelerythrine Bound to Fab BL3-6 S97N within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg204 b:145.7 occ:1.00 N2 R:G62 3.5 88.6 1.0 O4' R:A63 3.9 100.2 1.0 C1' R:A63 3.9 98.1 1.0 C1' R:C48 4.3 86.6 1.0 O2' R:A63 4.3 98.4 1.0 O2 R:C48 4.4 93.1 1.0 N3 R:G62 4.5 95.7 1.0 C2 R:G62 4.5 88.5 1.0 O4' R:C48 4.6 87.9 1.0 C4' R:A63 4.8 99.0 1.0 C2' R:A63 4.8 103.0 1.0 O2' R:C48 4.9 87.0 1.0 N9 R:A63 4.9 95.5 1.0 N1 R:C48 5.0 85.9 1.0 C2 R:C48 5.0 85.4 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