Magnesium in PDB 7d7y: Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)

The structure of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp), PDB code: 7d7y was solved by H.Chen, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.26 / 2.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.528, 57.703, 196.758, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 24

The binding sites of Magnesium atom in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) (pdb code 7d7y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp), PDB code: 7d7y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)


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 the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:67.7 occ:1.00 O A:HOH232 2.1 64.7 1.0 O A:HOH217 2.1 66.0 1.0 O A:HOH216 2.2 63.5 1.0 O A:HOH227 2.3 66.0 1.0 O2' A:G36 4.3 75.6 1.0 MG A:MG105 4.5 65.7 1.0 N7 A:G38 4.6 65.0 1.0 O A:HOH207 4.7 66.0 1.0 O6 A:G38 4.8 64.0 1.0 C2' A:G36 4.9 70.0 1.0 O A:HOH237 5.0 65.4 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)


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 the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:86.2 occ:1.00 O A:HOH206 2.1 79.3 1.0 O A:HOH226 2.1 86.9 1.0 O A:HOH236 2.2 92.7 1.0 O A:HOH213 2.3 75.7 1.0 O A:HOH238 2.3 75.6 1.0 O A:HOH239 2.4 95.2 1.0 OP1 A:A30 4.4 69.8 1.0 N7 A:G28 4.4 66.5 1.0 O6 A:G28 4.5 73.4 1.0 OP2 A:A30 4.8 66.3 1.0 C5 A:G28 4.9 67.6 1.0 C6 A:G28 5.0 69.0 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)


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 the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:65.7 occ:1.00 O A:HOH237 1.8 65.4 1.0 O A:HOH233 2.0 69.9 1.0 O A:HOH207 2.1 66.0 1.0 O A:HOH241 2.2 84.4 1.0 O A:HOH216 3.7 63.5 1.0 N4 A:C12 4.3 64.6 1.0 MG A:MG103 4.5 67.7 1.0 C5 A:C12 4.7 64.6 1.0 C4 A:C12 5.0 63.1 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)


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 the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:55.4 occ:1.00 O A:HOH218 2.0 63.4 1.0 OP1 A:U17 2.2 58.3 1.0 P A:U17 3.6 57.6 1.0 O3' A:G16 4.0 56.1 1.0 C5' A:U17 4.4 58.0 1.0 O5' A:U17 4.5 58.6 1.0 OP2 A:U17 4.7 59.8 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)


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 the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:69.9 occ:1.00 O A:HOH209 2.2 62.8 1.0 O A:HOH223 2.2 71.0 1.0 O A:HOH221 2.3 60.9 1.0 OP2 A:A7 2.4 66.8 1.0 O A:HOH220 2.4 69.9 1.0 O A:HOH234 2.4 66.2 1.0 P A:A7 3.6 65.5 1.0 O5' A:A7 4.0 63.9 1.0 OP1 A:G16 4.1 63.3 1.0 OP1 A:C15 4.4 63.9 1.0 OP1 A:A7 4.4 59.7 1.0 C8 A:A7 4.4 58.4 1.0 OP2 A:G16 4.7 61.0 1.0 C2' A:A7 4.8 59.3 1.0 O3' A:C6 4.8 68.2 1.0 N7 A:A7 4.9 57.3 1.0 P A:G16 4.9 62.0 1.0 C3' A:C6 5.0 67.1 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)


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 the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:71.5 occ:1.00 OP1 A:A8 1.9 62.3 1.0 O A:HOH210 2.0 69.3 1.0 O A:HOH219 2.1 64.3 1.0 O A:HOH214 2.1 62.6 1.0 O1B A:ATP102 2.2 81.0 1.0 O1A A:ATP102 2.2 72.8 1.0 PA A:ATP102 3.3 80.8 1.0 P A:A8 3.3 59.9 1.0 O1G A:ATP102 3.4 0.3 1.0 PB A:ATP102 3.4 94.6 1.0 O3A A:ATP102 3.7 87.2 1.0 O A:HOH204 3.8 61.4 1.0 OP2 A:A8 4.0 64.1 1.0 O2A A:ATP102 4.1 83.4 1.0 O5' A:A8 4.1 67.4 1.0 C5' A:A8 4.2 66.4 1.0 O3B A:ATP102 4.3 0.2 1.0 C3' A:A7 4.3 59.3 1.0 C5' A:A7 4.3 63.8 1.0 OP2 A:C15 4.4 61.3 1.0 O3' A:A7 4.4 58.6 1.0 PG A:ATP102 4.4 1.0 1.0 OP1 A:C14 4.4 67.4 1.0 C4' A:A7 4.5 64.0 1.0 O5' A:ATP102 4.6 75.6 1.0 O2B A:ATP102 4.6 91.4 1.0 OP1 A:A7 4.7 59.7 1.0 O2G A:ATP102 4.7 99.2 1.0 OP1 A:C15 4.8 63.9 1.0 O A:HOH208 5.0 60.6 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)


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 the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:66.5 occ:1.00 O A:HOH230 2.1 57.5 1.0 O A:HOH202 2.2 54.9 1.0 O A:HOH212 2.3 53.8 1.0 O6 A:G47 2.4 64.4 1.0 O A:HOH201 2.5 53.8 1.0 O A:HOH225 2.5 57.5 1.0 N7 A:G47 3.0 61.2 1.0 C6 A:G47 3.1 59.0 1.0 C5 A:G47 3.3 58.5 1.0 O4 A:U46 3.8 62.0 1.0 C4 A:U46 4.0 62.2 1.0 C5 A:U46 4.0 64.1 1.0 C8 A:G47 4.2 60.7 1.0 N1 A:G47 4.4 56.5 1.0 N7 A:G48 4.6 55.1 1.0 C4 A:G47 4.6 59.2 1.0 C6 A:U46 4.9 62.9 1.0 N3 A:U46 4.9 58.6 1.0 N4 A:C6 4.9 57.1 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp)


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 the DOMAIN1 of Nad+ Riboswitch with Adenosine Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:57.8 occ:1.00 N7 A:A10 1.9 56.8 1.0 OP2 A:C9 2.0 66.1 1.0 O A:HOH204 2.1 61.4 1.0 O A:HOH215 2.2 57.5 1.0 OP2 A:A8 2.2 64.1 1.0 O A:HOH208 2.3 60.6 1.0 C8 A:A10 2.9 53.8 1.0 C5 A:A10 3.0 59.4 1.0 P A:A8 3.4 59.9 1.0 N6 A:A10 3.4 61.0 1.0 P A:C9 3.4 64.9 1.0 O5' A:A8 3.6 67.4 1.0 C6 A:A10 3.6 60.0 1.0 N9 A:A10 4.1 54.5 1.0 C4 A:A10 4.1 58.8 1.0 OP2 A:C14 4.1 64.1 1.0 O5' A:C9 4.1 56.9 1.0 OP1 A:C9 4.3 58.7 1.0 OP1 A:A8 4.3 62.3 1.0 O3' A:A8 4.4 66.3 1.0 OP2 A:C15 4.4 61.3 1.0 O A:HOH214 4.6 62.6 1.0 O3' A:A7 4.6 58.6 1.0 C5 A:C9 4.7 59.2 1.0 C5 A:C15 4.8 61.4 1.0 C5' A:A8 4.8 66.4 1.0 C3' A:A8 4.9 60.7 1.0 C6 A:C9 4.9 60.8 1.0 N1 A:A10 4.9 58.7 1.0

H.Chen, M.Egger, X.Xu, L.Flemmich, O.Krasheninina, A.Sun, R.Micura, A.Ren. Structural Distinctions Between Nad+ Riboswitch Domains 1 and 2 Determine Differential Folding and Ligand Binding. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 33170270
DOI: 10.1093/NAR/GKAA1029