Magnesium in PDB 7d82: Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+

The structure of Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+, PDB code: 7d82 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)	27.52 / 2.49
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.916, 75.916, 50.289, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 27.1

The structure of Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ also contains other interesting chemical elements:

Manganese

(Mn)

7 atoms

The binding sites of Magnesium atom in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ (pdb code 7d82). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+, PDB code: 7d82:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+


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 DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:52.4 occ:1.00 O A:HOH229 1.8 56.4 1.0 N7 A:G36 2.0 54.1 1.0 O A:HOH220 2.1 60.1 1.0 O A:HOH231 2.3 56.0 1.0 O A:HOH228 2.8 51.4 1.0 C8 A:G36 2.8 46.8 1.0 C5 A:G36 3.2 51.0 1.0 O6 A:G36 3.7 53.4 1.0 C6 A:G36 3.8 52.1 1.0 N9 A:G36 4.1 49.5 1.0 C4 A:G36 4.2 48.7 1.0 O2 A:C14 5.0 40.2 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+


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 DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:60.2 occ:1.00 O A:HOH236 2.5 40.5 1.0 MG A:MG113 3.2 75.3 1.0 O A:HOH233 3.3 62.1 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+


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 DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:79.0 occ:1.00 O6 A:G34 2.1 84.0 1.0 C6 A:G34 3.0 83.4 1.0 N7 A:G33 3.3 79.7 1.0 C8 A:G33 3.3 85.4 1.0 N1 A:G34 3.8 78.6 1.0 OP2 A:G33 3.8 0.9 1.0 C5 A:G34 3.9 84.0 1.0 N7 A:A32 4.1 94.1 1.0 C5 A:A32 4.1 92.8 1.0 C6 A:A32 4.3 89.0 1.0 N7 A:G34 4.3 90.9 1.0 O5' A:G33 4.4 0.2 1.0 N6 A:A32 4.4 88.5 1.0 C5 A:G33 4.6 79.6 1.0 C8 A:A32 4.6 97.8 1.0 N9 A:G33 4.7 88.1 1.0 C4 A:A32 4.7 92.2 1.0 P A:G33 4.8 0.1 1.0 N1 A:A32 4.9 86.0 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+


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 DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg112 b:69.2 occ:1.00 OP2 A:A28 2.3 88.4 1.0 P A:A28 3.5 95.3 1.0 OP1 A:A28 3.9 90.1 1.0 C5' A:A28 4.2 83.3 1.0 O5' A:A28 4.2 87.3 1.0 OP1 A:G27 4.4 91.7 1.0 OP2 A:G27 4.5 87.8 1.0 O5' A:G27 4.6 91.1 1.0 P A:G27 4.7 91.4 1.0 O3' A:G27 4.8 87.3 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+


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 DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg113 b:75.3 occ:1.00 N7 A:G31 2.0 96.9 1.0 C8 A:G31 2.7 94.0 1.0 C5 A:G31 3.1 92.8 1.0 MG A:MG110 3.2 60.2 1.0 O6 A:G31 3.8 86.4 1.0 C6 A:G31 3.8 87.6 1.0 N9 A:G31 3.9 93.0 1.0 C4 A:G31 4.1 93.6 1.0 N7 A:A32 4.3 94.1 1.0 N6 A:A32 4.4 88.5 1.0 O A:HOH233 4.5 62.1 1.0 O5' A:G31 4.9 96.8 1.0 N2 A:G27 4.9 83.6 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+


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 DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg114 b:59.7 occ:1.00 O4' A:U44 3.6 47.0 1.0 N2 A:G16 3.7 39.1 1.0 MG A:MG115 3.7 60.4 1.0 O2' A:C43 3.8 39.8 1.0 O2 A:C43 3.9 40.6 1.0 C2' A:C43 4.3 36.8 1.0 C1' A:U44 4.4 47.6 1.0 C4' A:U44 4.6 41.4 1.0 C2 A:G16 4.9 39.1 1.0 C5' A:U44 4.9 37.4 1.0 C1' A:U17 5.0 36.7 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+


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 DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg115 b:60.4 occ:1.00 N3 A:G16 3.6 41.1 1.0 O2' A:G16 3.7 40.9 1.0 MG A:MG114 3.7 59.7 1.0 N2 A:G16 3.8 39.1 1.0 C2 A:G16 4.1 39.1 1.0 O4' A:U17 4.1 42.1 1.0 C1' A:U44 4.2 47.6 1.0 C2' A:G16 4.2 41.4 1.0 O2 A:U44 4.3 43.4 1.0 C1' A:G16 4.5 41.1 1.0 O4' A:U44 4.6 47.0 1.0 C4 A:G16 4.7 40.8 1.0 N1 A:U44 4.7 42.9 1.0 C2 A:U44 4.8 44.1 1.0 C1' A:U17 4.8 36.7 1.0 O2' A:U44 4.9 54.7 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