Magnesium in PDB 7els: Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine

The structure of Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine, PDB code: 7els 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)	40.05 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.721, 93.052, 40.052, 90, 90, 90
R / Rfree (%)	23.2 / 27.4

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>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine (pdb code 7els). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine, PDB code: 7els:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:65.4 occ:1.00 OP1 A:G7 1.9 82.5 1.0 O A:HOH201 2.1 70.2 1.0 O A:HOH210 2.9 65.0 1.0 P A:G7 3.3 75.8 1.0 O2' A:A6 3.3 68.9 1.0 OP2 A:G7 3.9 66.1 1.0 C2' A:A6 4.2 74.7 1.0 O5' A:G7 4.2 79.6 1.0 C3' A:A6 4.2 74.6 1.0 O3' A:A6 4.3 76.4 1.0 C5' A:G7 4.7 79.7 1.0 N7 A:G35 4.7 66.0 1.0 C8 A:G35 4.8 68.5 1.0 OP1 A:G36 4.9 72.3 1.0

Magnesium binding site 2 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:54.4 occ:1.00 O A:HOH218 1.9 58.9 1.0 O A:HOH211 1.9 59.9 1.0 O A:HOH204 2.0 71.5 1.0 OP2 A:A38 2.2 70.8 1.0 O A:HOH213 2.3 73.3 1.0 O A:HOH219 2.4 73.0 1.0 P A:A38 3.5 74.9 1.0 O5' A:A38 4.0 64.6 1.0 N7 A:A39 4.2 70.4 1.0 OP1 A:A38 4.2 81.0 1.0 N7 A:A38 4.3 66.4 1.0 O2' A:G35 4.3 70.9 1.0 C8 A:A38 4.5 69.2 1.0 O4 A:U40 4.5 66.5 1.0 OP2 A:A39 4.6 71.8 1.0 N9 A:AZA109 4.6 67.9 1.0 O3' A:A37 4.7 70.2 1.0 N6 A:A39 4.7 66.5 1.0 C3' A:A37 4.9 68.5 1.0

Magnesium binding site 3 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:67.3 occ:1.00 O A:HOH203 1.9 83.4 1.0 O A:HOH208 1.9 67.1 1.0 O A:HOH221 2.2 84.6 1.0 O A:HOH206 2.2 69.8 1.0 O6 A:AZA109 2.2 67.8 1.0 OP2 A:G7 2.3 66.1 1.0 N7 A:A8 3.5 78.4 1.0 C6 A:AZA109 3.5 68.7 1.0 P A:G7 3.8 75.8 1.0 N1 A:AZA109 4.2 68.3 1.0 O6 A:G10 4.2 71.8 1.0 N6 A:A8 4.2 83.5 1.0 O3' A:A6 4.3 76.4 1.0 O6 A:G35 4.3 79.4 1.0 O5' A:G7 4.4 79.6 1.0 O2' A:A6 4.4 68.9 1.0 C8 A:A8 4.4 79.9 1.0 O A:HOH201 4.5 70.2 1.0 C5 A:A8 4.5 86.0 1.0 C5 A:AZA109 4.6 64.8 1.0 OP2 A:A8 4.7 85.8 1.0 N3 A:A6 4.7 66.8 1.0 N7 A:G7 4.8 70.5 1.0 C8 A:G7 4.8 80.7 1.0 C6 A:A8 4.8 85.0 1.0 OP1 A:G7 4.9 82.5 1.0 C1' A:A6 4.9 72.0 1.0

Magnesium binding site 4 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:57.9 occ:1.00 O A:HOH209 2.1 60.7 1.0 OP1 A:C34 2.1 73.4 1.0 O A:HOH216 2.3 61.0 1.0 OP1 A:G36 2.5 72.3 1.0 OP1 A:G35 2.8 68.7 1.0 O5' A:G35 2.9 68.8 1.0 P A:G35 3.4 66.3 1.0 P A:C34 3.5 75.6 1.0 P A:G36 3.8 70.9 1.0 C5' A:G35 4.0 67.6 1.0 O3' A:C34 4.1 75.9 1.0 O3' A:G35 4.1 67.3 1.0 C5' A:C34 4.2 68.6 1.0 C3' A:G35 4.2 68.9 1.0 O5' A:C34 4.2 69.3 1.0 OP2 A:C34 4.3 68.1 1.0 O5' A:G36 4.4 67.4 1.0 O3' A:C33 4.5 68.8 1.0 C4' A:C34 4.7 73.0 1.0 C4' A:G35 4.7 69.3 1.0 OP2 A:G35 4.8 74.9 1.0 C3' A:C34 4.9 80.0 1.0

Magnesium binding site 5 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:73.6 occ:1.00 O A:HOH223 2.0 75.8 1.0 O A:HOH225 2.1 80.2 1.0 O A:HOH217 2.1 88.3 1.0 O A:HOH212 2.5 75.7 1.0 O A:HOH202 2.6 77.4 1.0 O A:HOH205 3.4 73.6 1.0 O6 A:G20 4.0 71.2 1.0 O6 A:G19 4.0 67.9 1.0 O6 A:G28 4.2 79.7 1.0 O6 A:G27 4.4 89.1 1.0 N4 A:C29 4.4 76.3 1.0 N7 A:G27 4.7 84.5 1.0 N7 A:G19 4.8 73.6 1.0 C6 A:G19 4.9 71.3 1.0 C6 A:G27 4.9 87.7 1.0 N7 A:G28 5.0 89.6 1.0

Magnesium binding site 6 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:94.7 occ:1.00 OP1 A:G2 2.4 90.2 1.0 O3' A:GTP101 3.7 95.0 1.0 P A:G2 3.7 94.4 1.0 C5' A:G2 3.8 78.3 1.0 O A:HOH215 3.8 85.4 1.0 O5' A:G2 4.0 84.1 1.0 OP2 A:G2 4.8 99.0 1.0 C3' A:GTP101 5.0 88.2 1.0

Magnesium binding site 7 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:92.9 occ:1.00 O2A B:GTP101 2.0 102.0 1.0 OP2 A:C46 2.4 77.2 1.0 O1A B:GTP101 2.7 97.5 1.0 PA B:GTP101 2.9 111.7 1.0 P A:C46 3.8 78.8 1.0 O5' B:GTP101 3.8 86.4 1.0 O2B B:GTP101 4.0 115.0 1.0 O3A B:GTP101 4.2 114.4 1.0 OP1 A:C46 4.4 81.5 1.0 O5' A:C46 4.7 79.9 1.0 PB B:GTP101 4.7 130.8 1.0 O1G B:GTP101 4.8 104.2 1.0 O3' A:C45 4.8 86.1 1.0 C5' B:GTP101 4.8 88.7 1.0 C3' A:C45 5.0 80.0 1.0

Magnesium binding site 8 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:94.8 occ:1.00 O B:HOH201 2.1 97.7 1.0 O6 B:AZA108 2.4 81.1 1.0 O B:HOH207 2.5 91.5 1.0 O B:HOH204 2.8 85.8 1.0 O B:HOH211 2.8 93.7 1.0 OP2 B:G7 2.9 96.4 1.0 O3' B:A6 3.7 96.5 1.0 O2' B:A6 3.7 84.2 1.0 C6 B:AZA108 3.8 81.4 1.0 P B:G7 3.9 102.4 1.0 N7 B:A8 4.1 95.5 1.0 N3 B:A6 4.1 82.2 1.0 O6 B:G10 4.3 85.3 1.0 C1' B:A6 4.3 87.6 1.0 OP2 B:A8 4.4 105.9 1.0 C2' B:A6 4.4 86.5 1.0 N1 B:AZA108 4.6 81.2 1.0 C5 B:AZA108 4.6 85.7 1.0 C3' B:A6 4.7 91.3 1.0 C8 B:G7 4.9 91.8 1.0 OP1 B:G7 4.9 96.5 1.0 N7 B:G7 4.9 92.9 1.0 C8 B:A8 4.9 96.0 1.0 N7 B:AZA108 4.9 85.9 1.0 C2 B:A6 4.9 84.8 1.0 O6 B:G35 5.0 93.8 1.0 N6 B:A8 5.0 89.5 1.0

Magnesium binding site 9 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:84.4 occ:1.00 O B:HOH208 2.1 98.5 1.0 OP2 B:A38 2.1 96.1 1.0 O B:HOH218 2.1 91.5 1.0 O B:HOH209 2.2 95.8 1.0 O B:HOH216 2.5 89.8 1.0 O B:HOH214 2.9 92.6 1.0 P B:A38 3.5 94.4 1.0 O5' B:A38 4.2 96.2 1.0 OP1 B:A38 4.2 96.7 1.0 O2' B:G35 4.3 94.0 1.0 C5' B:A37 4.5 97.8 1.0 O3' B:A37 4.5 98.3 1.0 C3' B:A37 4.7 98.4 1.0 OP2 B:A37 4.9 109.5 1.0

Magnesium binding site 10 out of 13 in the Crystal Structure of Xanthine Riboswitch with 8-Azaxanthine


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 Xanthine Riboswitch with 8-Azaxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:69.8 occ:1.00 OP1 B:C22 2.8 90.3 1.0 O B:HOH213 3.0 64.8 1.0 O B:HOH206 3.0 79.0 1.0 P B:C22 3.8 93.6 1.0 O5' B:C22 3.8 77.0 1.0 OP2 B:C22 4.4 71.1 1.0 C5' B:C22 4.4 83.7 1.0

X.Xu, M.Egger, H.Chen, K.Bartosik, R.Micura, A.Ren. Insights Into Xanthine Riboswitch Structure and Metal Ion-Mediated Ligand Recognition. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 34125892
DOI: 10.1093/NAR/GKAB486