Magnesium in PDB 7d81: Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)

The structure of Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), PDB code: 7d81 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)	30.36 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.026, 76.026, 50.468, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 25.1

The binding sites of Magnesium atom in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) (pdb code 7d81). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), PDB code: 7d81:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)


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+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:62.5 occ:1.00 OP2 A:A7 2.1 58.3 1.0 O A:HOH218 2.2 63.9 1.0 O A:HOH221 2.2 64.7 1.0 O A:HOH223 2.2 59.7 1.0 O A:HOH205 2.3 52.6 1.0 O A:HOH219 2.8 63.0 1.0 P A:A7 3.4 55.0 1.0 O5' A:A7 3.8 54.7 1.0 OP1 A:G16 3.8 48.1 1.0 OP2 A:G16 4.0 50.6 1.0 OP1 A:A7 4.1 55.2 1.0 C8 A:A7 4.4 53.6 1.0 P A:G16 4.4 48.0 1.0 C2' A:A7 4.5 52.8 1.0 OP1 A:C15 4.6 45.3 1.0 O3' A:C6 4.6 55.6 1.0 O A:HOH217 4.8 49.0 1.0 C3' A:C6 4.8 59.5 1.0 C5' A:C15 4.9 48.2 1.0 N7 A:A7 4.9 54.7 1.0 OP1 A:G37 4.9 50.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the DOMAIN2 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)


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+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:54.6 occ:1.00 OP2 A:C9 1.9 55.0 1.0 N7 A:A10 2.0 53.0 1.0 O A:HOH222 2.1 46.0 1.0 OP2 A:A8 2.1 49.2 1.0 O A:HOH210 2.2 52.0 1.0 O A:HOH211 2.3 42.2 1.0 C8 A:A10 2.8 57.3 1.0 C5 A:A10 3.2 49.4 1.0 P A:C9 3.3 61.8 1.0 P A:A8 3.4 48.1 1.0 N6 A:A10 3.8 49.1 1.0 C6 A:A10 3.9 48.9 1.0 O5' A:A8 3.9 48.9 1.0 OP2 A:C14 4.0 48.5 1.0 N9 A:A10 4.1 56.8 1.0 OP1 A:C9 4.1 63.6 1.0 O5' A:C9 4.2 62.2 1.0 OP1 A:A8 4.2 48.0 1.0 C4 A:A10 4.2 50.9 1.0 C5' A:A8 4.3 57.3 1.0 O3' A:A8 4.3 56.3 1.0 O A:HOH212 4.4 50.1 1.0 O A:HOH204 4.4 51.8 1.0 OP2 A:C15 4.4 51.3 1.0 O3' A:A7 4.6 54.5 1.0 C5 A:C9 4.6 57.2 1.0 C3' A:A8 4.6 58.2 1.0 C6 A:C9 4.9 55.0 1.0 OP1 A:C14 4.9 50.3 1.0 P A:C14 4.9 49.7 1.0 C5 A:C15 5.0 51.7 1.0

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


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+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:57.3 occ:1.00 O1N A:NAD104 1.8 61.6 1.0 O2A A:NAD104 1.9 56.4 1.0 O A:HOH204 2.1 51.8 1.0 OP1 A:A8 2.1 48.0 1.0 O A:HOH215 2.2 60.0 1.0 O A:HOH202 2.2 48.2 1.0 PN A:NAD104 3.1 71.3 1.0 PA A:NAD104 3.2 65.3 1.0 O3 A:NAD104 3.5 66.4 1.0 P A:A8 3.6 48.1 1.0 O A:HOH210 3.8 52.0 1.0 O5D A:NAD104 4.0 77.4 1.0 O5B A:NAD104 4.1 59.3 1.0 OP1 A:C14 4.2 50.3 1.0 OP2 A:C15 4.2 51.3 1.0 C5' A:A8 4.3 57.3 1.0 OP2 A:A8 4.3 49.2 1.0 O2N A:NAD104 4.3 67.4 1.0 O5' A:A8 4.4 48.9 1.0 O1A A:NAD104 4.4 72.8 1.0 OP1 A:C15 4.4 45.3 1.0 OP1 A:A7 4.5 55.2 1.0 C3' A:A7 4.6 53.5 1.0 O3' A:A7 4.6 54.5 1.0 C5' A:A7 4.6 57.7 1.0 C4' A:A7 4.8 54.6 1.0 P A:C15 4.8 49.3 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