Manganese in PDB 9uw0: Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok

The structure of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok, PDB code: 9uw0 was solved by X.Shen, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.50 / 1.97
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	47.206, 70.365, 116.266, 90, 90, 90
R / Rfree (%)	20.5 / 22.3

The structure of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok (pdb code 9uw0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok, PDB code: 9uw0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn102 b:48.4 occ:1.00 O6 X:G65 2.8 29.4 1.0 O X:HOH232 2.9 30.9 1.0 O6 X:G8 2.9 29.4 1.0 O4 X:U9 3.0 32.4 1.0 O4 X:U64 3.1 28.1 1.0 O X:HOH225 3.6 41.3 1.0 C4 X:U9 3.9 31.5 1.0 C6 X:G65 3.9 27.8 1.0 N3 X:U9 3.9 31.1 1.0 N6 X:A10 3.9 24.7 1.0 C6 X:G8 4.0 32.5 1.0 C4 X:U64 4.0 28.3 1.0 N4 X:C66 4.2 29.9 1.0 N7 X:G65 4.2 27.7 1.0 C5 X:G65 4.4 28.8 1.0 O X:HOH211 4.5 46.4 1.0 C5 X:U64 4.7 28.3 1.0 C6 X:A10 4.7 28.5 1.0 C5 X:G8 4.8 36.0 1.0 N3 X:U64 4.8 27.5 1.0 N1 X:G8 4.9 30.8 1.0 N7 X:G8 4.9 36.7 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn103 b:67.6 occ:1.00 N7 X:GTP5 2.3 39.2 1.0 O3G X:GTP5 2.3 64.2 1.0 C8 X:GTP5 3.1 40.3 1.0 O X:HOH215 3.4 47.8 1.0 C5 X:GTP5 3.4 37.0 1.0 PG X:GTP5 3.8 79.8 1.0 O6 X:GTP5 3.9 41.4 1.0 O2B X:GTP5 3.9 53.7 1.0 C6 X:GTP5 4.0 37.5 1.0 O3A X:GTP5 4.1 56.1 1.0 O1A X:GTP5 4.1 52.3 1.0 O X:HOH204 4.1 40.2 1.0 N9 X:GTP5 4.4 40.1 1.0 O3B X:GTP5 4.4 60.2 1.0 O1G X:GTP5 4.5 61.0 1.0 PB X:GTP5 4.5 60.5 1.0 C4 X:GTP5 4.5 39.8 1.0 PA X:GTP5 4.7 47.6 1.0 O2G X:GTP5 4.8 72.6 1.0 O5' X:GTP5 4.9 49.6 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn104 b:58.5 occ:1.00 OP1 X:A12 2.1 34.5 1.0 OP2 X:A10 2.1 35.6 1.0 O X:HOH229 2.1 46.2 1.0 O X:HOH234 2.3 42.3 1.0 O X:HOH231 2.3 47.1 1.0 O X:HOH227 2.5 37.4 1.0 P X:A12 3.4 37.9 1.0 P X:A10 3.5 40.1 1.0 OP2 X:A12 4.1 36.6 1.0 O X:HOH202 4.1 44.5 1.0 O5' X:A12 4.2 35.5 1.0 O5' X:U9 4.3 43.8 1.0 O3' X:U9 4.4 40.6 1.0 OP1 X:A10 4.4 43.2 1.0 C3' X:U9 4.4 38.5 1.0 O5' X:A10 4.4 33.1 1.0 O X:HOH212 4.5 35.2 1.0 O3' X:U11 4.6 34.9 1.0 C3' X:U11 4.7 31.1 1.0 OP2 X:U9 4.7 44.4 1.0 P X:U9 4.9 46.6 1.0 OP1 X:U9 4.9 47.4 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn105 b:61.8 occ:1.00 OP2 X:U13 2.3 41.2 1.0 P X:U13 3.6 43.3 1.0 OP1 X:U13 4.0 46.6 1.0 C5' X:A12 4.2 36.8 1.0 OP2 X:A12 4.3 36.6 1.0 O X:HOH210 4.3 31.5 1.0 C6 X:U13 4.4 38.3 1.0 O5' X:U13 4.5 41.9 1.0 C5' X:U13 4.5 39.3 1.0 O3' X:A12 4.6 38.3 1.0 C5 X:U13 4.7 39.0 1.0 N7 X:A62 4.7 33.9 1.0 O4' X:U13 4.8 43.8 1.0 C3' X:A12 5.0 37.5 1.0 C8 X:A62 5.0 30.6 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn106 b:46.1 occ:1.00 O X:HOH204 2.3 40.2 1.0 O2B X:GTP5 2.3 53.7 1.0 O1G X:GTP5 3.1 61.0 1.0 PB X:GTP5 3.2 60.5 1.0 O1B X:GTP5 3.6 57.7 1.0 O3B X:GTP5 3.7 60.2 1.0 PG X:GTP5 4.0 79.8 1.0 O3G X:GTP5 4.5 64.2 1.0 O3A X:GTP5 4.7 56.1 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn107 b:69.6 occ:1.00 N7 X:G27 2.4 49.9 1.0 C8 X:G27 3.3 50.8 1.0 C5 X:G27 3.5 49.6 1.0 O6 X:G27 3.7 52.1 1.0 N7 X:G26 3.8 53.1 1.0 C6 X:G27 4.0 45.7 1.0 C8 X:G26 4.3 56.9 1.0 N9 X:G27 4.5 52.4 1.0 C5 X:G26 4.5 53.0 1.0 OP2 X:G26 4.5 82.0 1.0 C4 X:G27 4.6 52.4 1.0 O6 X:G26 4.9 55.4 1.0 C6 X:G26 5.0 53.4 1.0

X.Shen, H.Li, X.Xu, Q.Song, X.Tai, M.He, A.Ren. Structure-Based Insights Into the Ligand Specificity Tuning of 2'-Dg-III Riboswitch. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40795954
DOI: 10.1093/NAR/GKAF773