Magnesium in PDB 7d7x: Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Diphosphate (Adp)

The structure of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Diphosphate (Adp), PDB code: 7d7x 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)	26.64 / 2.63
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.337, 57.400, 196.826, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Adenosine Diphosphate (Adp) (pdb code 7d7x). 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 Diphosphate (Adp), PDB code: 7d7x:
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 Diphosphate (Adp)


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:66.5 occ:1.00 O A:HOH203 1.7 63.4 1.0 O A:HOH221 2.1 73.6 1.0 OP2 A:A11 2.3 71.2 1.0 O A:HOH219 2.4 74.0 1.0 P A:A11 3.7 72.8 1.0 OP1 A:A10 4.2 73.8 1.0 OP1 A:A11 4.4 78.5 1.0 C3' A:A10 4.4 66.6 1.0 O5' A:A11 4.6 72.9 1.0 O3' A:A10 4.6 69.0 1.0 C5' A:A11 4.7 72.4 1.0 C5' A:A10 4.8 61.5 1.0 C4' A:A10 4.9 68.1 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:92.4 occ:1.00 O A:HOH231 2.1 89.9 1.0 O A:HOH208 2.1 85.5 1.0 O A:HOH209 2.1 80.4 1.0 O A:HOH239 2.5 82.2 1.0 O A:HOH214 2.5 82.2 1.0 O A:HOH238 2.5 99.0 1.0 OP1 A:A30 4.1 82.5 1.0 N7 A:G28 4.2 81.8 1.0 O6 A:G28 4.2 78.1 1.0 OP2 A:A30 4.5 78.1 1.0 C5 A:G28 4.8 78.0 1.0 C6 A:G28 4.8 76.5 1.0 P A:A30 4.8 83.1 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:77.6 occ:1.00 O A:HOH235 2.1 84.4 1.0 O A:HOH226 2.5 81.2 1.0 N1 A:A29 4.2 75.5 1.0 MG A:MG107 4.4 92.6 1.0 C2 A:A29 4.6 77.3 1.0 O A:HOH230 4.7 89.4 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:80.3 occ:1.00 O A:HOH211 2.2 76.6 1.0 OP2 A:A7 2.3 74.2 1.0 O A:HOH225 2.3 81.8 1.0 O A:HOH224 2.3 74.2 1.0 O A:HOH216 2.4 76.8 1.0 O A:HOH215 2.4 81.7 1.0 P A:A7 3.6 73.1 1.0 OP1 A:G16 3.7 72.7 1.0 O5' A:A7 4.0 73.2 1.0 C8 A:A7 4.3 68.2 1.0 OP2 A:G16 4.3 72.9 1.0 OP1 A:A7 4.5 69.9 1.0 P A:G16 4.5 74.0 1.0 OP1 A:C15 4.5 74.1 1.0 C2' A:A7 4.6 67.2 1.0 N7 A:A7 4.7 69.0 1.0 O3' A:C6 4.7 73.1 1.0 C3' A:C6 4.9 78.7 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:76.8 occ:1.00 OP1 A:A8 1.7 75.1 1.0 O A:HOH217 1.9 69.6 1.0 O1B A:ADP110 2.1 90.0 1.0 O A:HOH205 2.3 66.2 1.0 O A:HOH202 2.3 75.8 1.0 O1A A:ADP110 2.6 80.8 1.0 P A:A8 3.0 74.2 1.0 PB A:ADP110 3.4 1.0 1.0 O A:HOH207 3.5 73.5 1.0 OP2 A:A8 3.7 64.7 1.0 O5' A:A8 3.7 76.3 1.0 PA A:ADP110 3.7 94.3 1.0 O3A A:ADP110 3.7 94.3 1.0 C5' A:A8 3.8 75.0 1.0 OP2 A:C15 4.1 72.2 1.0 O2B A:ADP110 4.1 91.9 1.0 O5' A:ADP110 4.1 83.3 1.0 O3' A:A7 4.2 68.2 1.0 C3' A:A7 4.3 65.9 1.0 C5' A:A7 4.4 74.5 1.0 C4' A:A7 4.4 71.2 1.0 OP1 A:C14 4.4 73.3 1.0 O A:HOH212 4.5 65.0 1.0 O3B A:ADP110 4.5 0.6 1.0 OP1 A:C15 4.8 74.1 1.0 OP1 A:A7 4.8 69.9 1.0 MG A:MG108 4.8 72.0 1.0 P A:C15 4.9 67.9 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:92.6 occ:1.00 O A:HOH230 2.7 89.4 1.0 O A:HOH235 3.6 84.4 1.0 MG A:MG104 4.4 77.6 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:72.0 occ:1.00 OP2 A:A8 1.9 64.7 1.0 N7 A:A10 1.9 67.4 1.0 O A:HOH213 2.0 67.7 1.0 OP2 A:C9 2.1 71.8 1.0 O A:HOH207 2.2 73.5 1.0 O A:HOH212 2.3 65.0 1.0 C8 A:A10 3.0 66.0 1.0 C5 A:A10 3.0 66.2 1.0 P A:A8 3.3 74.2 1.0 N6 A:A10 3.4 69.1 1.0 P A:C9 3.5 72.9 1.0 C6 A:A10 3.6 69.8 1.0 N9 A:A10 4.1 67.4 1.0 C4 A:A10 4.2 69.4 1.0 OP2 A:C15 4.2 72.2 1.0 OP1 A:A8 4.2 75.1 1.0 O5' A:A8 4.2 76.3 1.0 O3' A:A7 4.2 68.2 1.0 O A:HOH202 4.3 75.8 1.0 OP1 A:C9 4.3 69.9 1.0 O5' A:C9 4.4 63.1 1.0 OP2 A:C14 4.4 75.4 1.0 C5 A:C9 4.4 66.2 1.0 C5' A:A8 4.4 75.0 1.0 O3' A:A8 4.4 74.0 1.0 C3' A:A8 4.6 67.6 1.0 C6 A:C9 4.8 69.3 1.0 MG A:MG106 4.8 76.8 1.0 N1 A:A10 4.9 69.5 1.0 C5 A:C15 4.9 72.2 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:72.9 occ:1.00 O6 A:G47 1.9 72.6 1.0 O A:HOH234 2.1 84.5 1.0 O A:HOH218 2.2 66.4 1.0 O A:HOH201 2.2 64.8 1.0 O A:HOH206 2.3 63.7 1.0 O A:HOH228 2.4 64.3 1.0 C6 A:G47 2.9 68.3 1.0 C5 A:G47 3.5 68.1 1.0 N7 A:G47 3.5 67.4 1.0 O4 A:U46 3.9 70.4 1.0 N4 A:C6 4.0 58.5 1.0 N1 A:G47 4.1 65.7 1.0 O6 A:G48 4.3 73.1 1.0 N7 A:G48 4.3 68.0 1.0 C4 A:U46 4.4 71.2 1.0 C5 A:U46 4.7 72.7 1.0 C8 A:G47 4.8 68.4 1.0 C4 A:G47 4.8 67.6 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