Magnesium in PDB 9iwf: Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine

The structure of Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine, PDB code: 9iwf was solved by X.C.Xu, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.56 / 2.06
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.585, 115.752, 126.759, 90, 90, 90
R / Rfree (%)	21.9 / 25.4

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>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine (pdb code 9iwf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine, PDB code: 9iwf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


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 P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:44.2 occ:1.00 O A:HOH227 1.9 52.0 1.0 O B:HOH265 2.3 60.3 1.0 O A:HOH202 2.7 60.6 1.0 O A:HOH221 2.7 57.6 1.0 O1B A:GTP101 3.8 64.7 1.0 OP1 A:U65 4.0 42.5 1.0 O1A A:GTP101 4.1 64.6 1.0 O2B A:GTP101 4.2 68.7 1.0 OP2 A:U65 4.3 40.6 1.0 OP2 B:C70 4.6 52.5 1.0 P A:U65 4.7 38.9 1.0 PB A:GTP101 4.7 77.2 1.0

Magnesium binding site 2 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


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 P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:38.1 occ:1.00 O A:HOH224 1.9 35.3 1.0 O A:HOH220 2.0 40.0 1.0 O A:HOH229 2.0 36.9 1.0 O A:HOH214 2.0 38.7 1.0 OP1 A:G3 2.1 37.8 1.0 P A:G3 3.4 40.2 1.0 OP2 A:G3 4.0 38.6 1.0 O5' A:G3 4.2 35.9 1.0 O A:HOH213 4.2 36.7 1.0 OP2 A:U4 4.3 35.6 1.0 O A:HOH201 4.3 38.3 1.0 OP1 A:G63 4.4 30.4 1.0 C5' A:G3 4.5 35.5 1.0 O3' A:G2 4.5 33.1 1.0 O A:HOH206 4.6 34.0 1.0

Magnesium binding site 3 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


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 P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:39.4 occ:1.00 O A:HOH223 2.0 40.5 1.0 O A:HOH222 2.1 39.7 1.0 O A:HOH209 2.1 37.1 1.0 O A:HOH219 2.1 38.8 1.0 OP2 A:A9 2.2 35.1 1.0 O A:HOH234 2.2 44.6 1.0 P A:A9 3.5 42.7 1.0 MG A:MG108 3.9 34.9 1.0 O A:HOH216 3.9 42.1 1.0 O5' A:A9 4.1 43.7 1.0 N7 A:G62 4.1 34.5 1.0 C5' A:A9 4.1 43.9 1.0 O6 A:G62 4.2 36.1 1.0 OP1 A:A9 4.2 39.2 1.0 OP2 A:A61 4.3 40.1 1.0 O6 A:G63 4.4 34.5 1.0 O3' A:U8 4.5 37.5 1.0 OP2 A:A10 4.7 43.4 1.0 N7 A:A61 4.7 35.9 1.0 C5 A:G62 4.9 33.8 1.0 C6 A:G62 4.9 33.9 1.0

Magnesium binding site 4 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


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 P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:58.5 occ:1.00 O A:HOH236 1.9 56.7 1.0 O A:HOH231 2.1 53.1 1.0 O A:HOH240 2.1 54.7 1.0 O A:HOH239 2.7 49.9 1.0 OP2 A:C31 4.2 60.4 1.0 N7 A:G32 4.7 47.2 1.0 O4 A:U33 4.8 44.4 1.0

Magnesium binding site 5 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


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 P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:58.7 occ:1.00 O A:HOH243 2.0 49.8 1.0 O A:HOH205 2.0 45.5 1.0 O A:HOH238 2.6 53.8 1.0 O A:HOH207 2.7 36.5 1.0 O A:HOH215 2.7 56.4 1.0 O6 A:G43 3.8 37.0 1.0 O6 A:G56 3.9 40.8 1.0 N4 A:C57 4.1 36.0 1.0 O6 A:G42 4.4 33.8 1.0 N4 A:C44 4.6 40.6 1.0 N7 A:G42 4.8 34.8 1.0 C6 A:G56 4.9 40.6 1.0

Magnesium binding site 6 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


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 P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:44.1 occ:1.00 O2' A:C70 1.9 49.5 1.0 O3' A:C70 1.9 44.9 1.0 C2' A:C70 2.7 44.6 1.0 C3' A:C70 2.8 39.5 1.0 C4' A:C70 3.8 41.6 1.0 C1' A:C70 4.0 40.3 1.0 O4' A:C70 4.5 38.6 1.0 O2' B:GTP101 4.8 50.5 1.0 C5' A:C70 5.0 38.6 1.0

Magnesium binding site 7 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


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 P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:34.9 occ:1.00 O A:HOH216 1.9 42.1 1.0 O A:HOH211 1.9 36.9 1.0 O6 A:G63 2.7 34.5 1.0 OP2 A:A9 2.8 35.1 1.0 O6 A:XAN110 3.0 33.5 1.0 O A:HOH209 3.0 37.1 1.0 O3' A:U8 3.1 37.5 1.0 O2' A:U8 3.2 37.4 1.0 P A:A9 3.6 42.7 1.0 O A:HOH222 3.8 39.7 1.0 C6 A:G63 3.9 33.6 1.0 MG A:MG104 3.9 39.4 1.0 C2' A:U8 4.1 38.3 1.0 C6 A:XAN110 4.1 37.5 1.0 C3' A:U8 4.1 40.6 1.0 N4 A:C64 4.3 30.2 1.0 C1' A:U8 4.4 38.1 1.0 O2 A:U8 4.4 38.5 1.0 N1 A:G63 4.5 29.3 1.0 C5' A:A9 4.7 43.9 1.0 O5' A:A9 4.7 43.7 1.0 OP1 A:A9 4.7 39.2 1.0 C5 A:XAN110 4.9 35.7 1.0 N7 A:XAN110 4.9 36.3 1.0 O A:HOH223 4.9 40.5 1.0

Magnesium binding site 8 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:68.7 occ:1.00 O2' A:U34 3.6 53.5 1.0 O4' A:U35 4.1 50.5 1.0 C2' A:U34 4.7 49.9 1.0 O4' A:C67 4.8 35.0 1.0 N1 A:U35 4.8 40.8 1.0 C2 A:U35 4.8 35.2 1.0 O2' A:C67 4.8 40.3 1.0 C4' A:C67 4.9 39.8 1.0

Magnesium binding site 9 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:38.6 occ:1.00 O B:HOH239 1.8 54.1 1.0 O B:HOH208 2.0 53.6 1.0 O A:HOH232 2.1 62.4 1.0 O B:HOH258 2.2 55.3 1.0 O B:HOH209 2.5 50.9 1.0 O B:HOH204 3.0 62.4 1.0 O6 B:G2 3.9 39.5 1.0 N7 B:GTP101 4.0 46.2 1.0 O1G B:GTP101 4.1 66.6 1.0 O6 B:GTP101 4.4 41.8 1.0 O3A A:GTP101 4.4 64.1 1.0 N4 B:C70 4.6 43.5 1.0 O2A A:GTP101 4.7 60.2 1.0 C6 B:G2 4.7 38.1 1.0 O6 A:G2 4.8 35.8 1.0 O3A B:GTP101 4.8 63.6 1.0 O5' A:GTP101 4.8 58.4 1.0 N7 B:G2 4.9 45.2 1.0 O1A B:GTP101 4.9 64.7 1.0 C5 B:GTP101 4.9 45.4 1.0 C8 B:GTP101 4.9 48.2 1.0 PA A:GTP101 4.9 68.4 1.0

Magnesium binding site 10 out of 15 in the Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of P. Beijingensis Xanthine-II Riboswitch in Complex with Xanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:46.5 occ:1.00 OP2 B:A9 2.1 38.1 1.0 O B:HOH247 2.2 48.0 1.0 O B:HOH248 2.2 50.5 1.0 O B:HOH233 2.3 38.6 1.0 O B:HOH215 2.4 41.0 1.0 O B:HOH201 2.5 42.7 1.0 P B:A9 3.4 35.6 1.0 O5' B:A9 3.9 34.7 1.0 C5' B:A9 4.1 36.7 1.0 OP1 B:A9 4.2 32.4 1.0 OP2 B:A61 4.3 57.9 1.0 N7 B:G62 4.4 32.4 1.0 O6 B:G62 4.5 32.1 1.0 O B:HOH230 4.5 28.0 1.0 O3' B:U8 4.5 38.5 1.0 O6 B:G63 4.6 34.6 1.0 N7 B:A61 4.7 39.2 1.0 OP2 B:A10 4.8 34.1 1.0

X.Xu, M.He, X.Tai, Q.Ren, X.Shen, C.Li, A.Ren. Structure-Based Principles Underlying Ligand Recognition of Xanthine-II Riboswitch. Sci China Life Sci 2025.
ISSN: ESSN 1869-1889
PubMed: 40304919
DOI: 10.1007/S11427-024-2800-0