Magnesium in PDB 7d7v: Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein

The structure of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein, PDB code: 7d7v 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)	50.00 / 2.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.593, 68.593, 333.848, 90.00, 90.00, 120.00
R / Rfree (%)	25 / 30.8

The binding sites of Magnesium atom in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein (pdb code 7d7v). 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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein, PDB code: 7d7v:
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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein


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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:50.7 occ:1.00 O A:HOH209 2.0 54.0 1.0 O C:HOH202 2.0 49.7 1.0 O A:HOH213 2.1 48.3 1.0 O C:HOH201 2.2 46.5 1.0 O A:HOH232 2.2 53.9 1.0 O A:HOH218 2.2 48.5 1.0 N4 A:C25 3.0 52.8 1.0 O A:HOH216 4.0 44.0 1.0 C4 A:C25 4.2 52.3 1.0 N7 A:G24 4.4 52.1 1.0 O6 A:G24 4.4 53.8 1.0 O A:HOH220 4.5 47.2 1.0 O6 A:G40 4.5 48.2 1.0 C5 A:C25 4.6 52.1 1.0 O6 A:G26 4.6 46.7 1.0 C5 A:G24 4.9 50.0 1.0 MG A:MG103 4.9 50.3 1.0 C6 A:G24 4.9 49.9 1.0 O A:HOH235 4.9 62.0 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein


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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:50.3 occ:1.00 O A:HOH235 1.9 62.0 1.0 O A:HOH216 1.9 44.0 1.0 O A:HOH239 2.0 47.2 1.0 O A:HOH223 2.1 48.5 1.0 O A:HOH215 2.2 51.4 1.0 O A:HOH220 2.2 47.2 1.0 O A:HOH213 4.1 48.3 1.0 O6 A:G23 4.5 50.5 1.0 O6 A:G24 4.8 53.8 1.0 O A:HOH232 4.9 53.9 1.0 N7 A:G23 4.9 48.1 1.0 MG A:MG102 4.9 50.7 1.0 N7 A:G22 5.0 49.0 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein


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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:51.1 occ:1.00 O A:HOH237 2.0 51.5 1.0 O A:HOH238 2.1 55.5 1.0 O A:HOH228 2.1 46.3 1.0 O A:HOH205 2.1 54.1 1.0 O A:HOH227 2.3 54.8 1.0 O A:HOH225 2.3 54.1 1.0 C5 A:C17 3.8 45.7 1.0 N7 A:G18 3.9 46.2 1.0 N4 A:C17 4.2 45.6 1.0 C4 A:C17 4.3 45.4 1.0 O6 A:G18 4.4 46.1 1.0 OP2 A:C17 4.5 55.2 1.0 C6 A:C17 4.6 48.0 1.0 C5 A:G18 4.8 43.5 1.0 C8 A:G18 4.8 48.5 1.0 C6 A:G18 5.0 46.4 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein


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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:49.9 occ:1.00 O A:HOH236 2.0 57.0 1.0 O A:HOH201 2.0 50.4 1.0 O A:HOH230 2.1 49.4 1.0 O A:HOH234 2.1 43.5 1.0 O A:HOH214 2.2 57.8 1.0 O A:HOH221 2.3 45.4 1.0 C5 A:C49 3.7 42.1 1.0 C4 A:C49 4.0 44.5 1.0 OP2 A:G50 4.1 58.8 1.0 N4 A:C49 4.2 42.0 1.0 C6 A:C49 4.3 48.5 1.0 OP2 A:C49 4.3 46.0 1.0 N7 A:G50 4.3 46.5 1.0 N3 A:C49 4.9 49.0 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein


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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:60.3 occ:1.00 O A:HOH208 1.9 57.2 1.0 O A:HOH229 2.0 69.3 1.0 O A:HOH224 2.0 65.5 1.0 O A:HOH212 2.0 64.0 1.0 OP2 A:A6 2.0 61.6 1.0 O A:HOH204 2.2 68.4 1.0 P A:A6 3.4 55.2 1.0 O5' A:A6 3.9 51.7 1.0 C8 A:A6 4.2 50.7 1.0 OP1 A:A6 4.3 52.5 1.0 O3' A:C5 4.5 53.3 1.0 N7 A:A6 4.6 46.3 1.0 OP1 A:G15 4.6 53.8 1.0 C3' A:C5 4.7 52.0 1.0 C2' A:A6 4.9 52.4 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein


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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:58.2 occ:1.00 OP2 A:C8 1.7 64.5 1.0 OP2 A:A7 1.8 49.6 1.0 N7 A:A9 1.9 60.8 1.0 O A:HOH203 1.9 55.7 1.0 O A:HOH206 2.0 59.8 1.0 O A:HOH207 2.0 55.7 1.0 C8 A:A9 2.8 62.5 1.0 C5 A:A9 3.0 57.4 1.0 P A:C8 3.2 60.5 1.0 P A:A7 3.2 52.9 1.0 N6 A:A9 3.4 57.4 1.0 C6 A:A9 3.6 54.5 1.0 OP1 A:C8 3.9 58.6 1.0 OP1 A:A7 4.0 55.5 1.0 O5' A:C8 4.1 61.5 1.0 O5' A:A7 4.1 64.8 1.0 N9 A:A9 4.1 59.7 1.0 O3' A:A7 4.1 52.5 1.0 C5' A:A7 4.1 59.4 1.0 C5 A:C8 4.1 59.7 1.0 C4 A:A9 4.1 61.2 1.0 C3' A:A7 4.2 56.2 1.0 O3' A:A6 4.3 61.0 1.0 O A:HOH202 4.4 63.8 1.0 C6 A:C8 4.5 63.7 1.0 OP2 A:C13 4.7 52.6 1.0 C4' A:A7 4.8 55.1 1.0 N1 A:A9 4.9 58.0 1.0 OP2 A:C14 5.0 56.0 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein


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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:58.7 occ:1.00 O1N A:NAD110 2.0 72.7 1.0 O A:HOH210 2.0 61.0 1.0 O A:HOH211 2.1 66.1 1.0 O A:HOH202 2.1 63.8 1.0 O1A A:NAD110 2.1 60.0 1.0 OP1 A:A7 2.2 55.5 1.0 PN A:NAD110 3.4 78.6 1.0 PA A:NAD110 3.5 65.8 1.0 P A:A7 3.7 52.9 1.0 O3 A:NAD110 3.9 69.5 1.0 O A:HOH207 4.1 55.7 1.0 OP1 A:C13 4.2 60.4 1.0 O5' A:A7 4.2 64.8 1.0 OP1 A:A6 4.3 52.5 1.0 OP1 A:C14 4.4 52.9 1.0 O5D A:NAD110 4.4 85.5 1.0 C5' A:A6 4.4 55.7 1.0 O A:HOH206 4.4 59.8 1.0 O2N A:NAD110 4.4 74.7 1.0 O2A A:NAD110 4.4 65.6 1.0 C3' A:A6 4.5 54.7 1.0 OP2 A:C14 4.5 56.0 1.0 C5' A:A7 4.5 59.4 1.0 O5B A:NAD110 4.5 55.1 1.0 OP2 A:A7 4.6 49.6 1.0 O3' A:A6 4.6 61.0 1.0 C4' A:A6 4.7 57.1 1.0 P A:C14 4.8 62.4 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein


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 Nicotinamide Adenine Dinucleotide (Nad+) and U1A Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:76.8 occ:1.00 O A:HOH217 2.2 65.6 1.0 O A:HOH222 2.2 71.9 1.0 O A:HOH226 2.3 76.7 1.0 O A:HOH231 2.3 69.7 1.0 O A:HOH233 2.3 73.0 1.0 O A:HOH219 2.3 66.8 1.0 N3 A:C14 4.0 59.5 1.0 O6 A:G43 4.2 66.1 1.0 OP1 A:U10 4.5 83.0 1.0 N4 A:C14 4.6 57.5 1.0 C6 A:G43 4.6 61.7 1.0 O2 A:C14 4.7 63.1 1.0 O3' A:A9 4.7 72.4 1.0 C4 A:C14 4.8 56.2 1.0 C2 A:C14 4.8 56.7 1.0 N7 A:G43 4.9 68.2 1.0 C5 A:G43 4.9 64.9 1.0 N4 A:C13 5.0 53.7 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