Osmium 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:

Magnesium	(Mg)	5 atoms
Potassium	(K)	1 atom

The binding sites of Osmium 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 Osmium atom.
In total 4 binding sites of Osmium where determined in the Yjdf Riboswitch From R. Gauvreauii in Complex with Chelerythrine Bound to Fab BL3-6 S97N, PDB code: 8uiw:
Jump to Osmium binding site number: 1; 2; 3; 4;

Osmium binding site 1 out of 4 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 Osmium with other atoms in the Os 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 B:Os301 b:176.1 occ:0.29 CE B:LYS189 2.7 218.2 1.0 CD B:LYS189 2.9 213.6 1.0 OS B:OS302 3.4 175.5 0.3 CG B:LYS189 3.9 204.2 1.0 CE1 B:HIS190 3.9 217.3 1.0 NZ B:LYS189 4.1 202.5 1.0 ND1 B:HIS190 4.4 205.0 1.0 OD2 B:ASP186 4.4 222.4 1.0 NE2 B:HIS190 4.8 226.8 1.0

Osmium binding site 2 out of 4 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 Osmium with other atoms in the Os 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 B:Os302 b:175.5 occ:0.32 NE2 B:HIS190 3.3 226.8 1.0 OS B:OS301 3.4 176.1 0.3 CE1 B:HIS190 3.4 217.3 1.0 CB B:ALA154 3.6 209.0 1.0 CE B:LYS189 3.6 218.2 1.0 CD2 B:HIS190 4.0 221.4 1.0 NZ B:LYS189 4.2 202.5 1.0 ND1 B:HIS190 4.2 205.0 1.0 CG B:HIS190 4.5 210.3 1.0 O B:ALA154 4.6 197.0 1.0 OE1 B:GLN156 4.7 193.4 1.0 CD B:LYS189 4.9 213.6 1.0 CA B:ALA154 4.9 204.3 1.0

Osmium binding site 3 out of 4 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 Osmium with other atoms in the Os 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 L:Os302 b:144.9 occ:0.28 NE2 L:HIS190 2.3 153.3 1.0 CE1 L:HIS190 2.8 152.1 1.0 CD2 L:HIS190 3.2 149.4 1.0 ND1 L:HIS190 3.7 151.3 1.0 CG L:HIS190 4.0 147.0 1.0 CG1 L:VAL151 4.9 138.2 1.0 OE1 L:GLN156 5.0 150.4 1.0

Osmium binding site 4 out of 4 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 Osmium with other atoms in the Os 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 L:Os303 b:162.4 occ:0.22 N L:ASP2 2.2 132.5 1.0 CA L:SER1 2.6 138.2 1.0 C L:SER1 2.8 133.3 1.0 OG L:SER1 3.2 128.7 1.0 CA L:ASP2 3.4 128.1 1.0 CB L:SER1 3.4 137.5 1.0 OD1 L:ASP2 3.5 138.4 1.0 CB L:ASP2 3.6 123.1 1.0 CG L:ASP2 3.7 132.4 1.0 N L:SER1 3.7 112.1 1.0 O L:SER1 4.0 138.1 1.0 O L:ASP2 4.2 123.2 1.0 C L:ASP2 4.3 113.6 1.0 OD2 L:ASP2 4.4 129.2 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