Manganese 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:

Magnesium

(Mg)

7 atoms

The binding sites of Manganese 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 Manganese atom.
In total 7 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese 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 Manganese with other atoms in the Mn 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:Mn101 b:50.5 occ:1.00 O1N A:NAD108 2.0 52.0 1.0 O A:HOH206 2.1 43.9 1.0 OP1 A:A8 2.1 47.4 1.0 O1A A:NAD108 2.1 45.5 1.0 O A:HOH211 2.2 46.1 1.0 O A:HOH232 2.7 47.7 1.0 PN A:NAD108 3.4 54.9 1.0 PA A:NAD108 3.4 50.8 1.0 P A:A8 3.5 46.1 1.0 O A:HOH225 3.6 43.0 1.0 O3 A:NAD108 3.8 52.0 1.0 O5' A:A8 4.1 47.1 1.0 O5D A:NAD108 4.2 64.9 1.0 OP1 A:C14 4.2 42.0 1.0 OP2 A:C15 4.2 48.3 1.0 C5' A:A8 4.3 42.4 1.0 O5B A:NAD108 4.3 51.9 1.0 OP2 A:A8 4.4 43.8 1.0 OP1 A:C15 4.5 42.4 1.0 C5' A:A7 4.5 44.6 1.0 C3' A:A7 4.5 46.0 1.0 O2N A:NAD108 4.6 62.3 1.0 O3' A:A7 4.6 41.7 1.0 OP1 A:A7 4.6 43.5 1.0 O2A A:NAD108 4.6 49.1 1.0 C4' A:A7 4.7 47.8 1.0 P A:C15 4.9 42.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn102 b:43.8 occ:1.00 OP2 A:C9 2.0 46.6 1.0 O A:HOH217 2.0 45.2 1.0 OP2 A:A8 2.1 43.8 1.0 O A:HOH225 2.2 43.0 1.0 O A:HOH222 2.2 40.3 1.0 N7 A:A10 2.3 44.0 1.0 C8 A:A10 3.1 43.8 1.0 P A:C9 3.4 49.6 1.0 P A:A8 3.4 46.1 1.0 C5 A:A10 3.4 43.3 1.0 N6 A:A10 3.9 46.3 1.0 C5' A:A8 4.0 42.4 1.0 OP2 A:C14 4.0 48.8 1.0 OP1 A:A8 4.0 47.4 1.0 OP1 A:C9 4.0 52.7 1.0 O5' A:A8 4.1 47.1 1.0 C6 A:A10 4.1 43.9 1.0 O A:HOH206 4.3 43.9 1.0 O5' A:C9 4.3 52.8 1.0 N9 A:A10 4.3 45.0 1.0 O3' A:A8 4.3 40.5 1.0 C4 A:A10 4.5 41.4 1.0 C3' A:A8 4.5 46.3 1.0 OP1 A:C14 4.5 42.0 1.0 OP2 A:C15 4.5 48.3 1.0 O3' A:A7 4.6 41.7 1.0 C5 A:C9 4.6 46.9 1.0 P A:C14 4.7 40.7 1.0 C4' A:A8 4.8 44.7 1.0 C6 A:C9 5.0 48.5 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn103 b:54.0 occ:1.00 O A:HOH224 1.7 50.9 1.0 OP2 A:A7 2.1 36.3 1.0 O A:HOH201 2.2 49.1 1.0 O A:HOH210 2.3 50.9 1.0 O A:HOH219 2.3 51.2 1.0 O A:HOH215 2.4 48.3 1.0 P A:A7 3.2 47.5 1.0 OP1 A:A7 3.6 43.5 1.0 O5' A:A7 3.8 53.0 1.0 OP1 A:C15 3.9 42.4 1.0 OP1 A:G16 4.0 42.1 1.0 OP2 A:G16 4.3 39.3 1.0 O3' A:C6 4.6 48.2 1.0 C5' A:C15 4.6 39.0 1.0 P A:G16 4.7 38.8 1.0 OP1 A:G37 4.8 44.6 1.0 C2' A:A7 4.9 47.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn104 b:72.0 occ:1.00 O A:HOH214 2.0 41.3 1.0 O A:HOH208 2.2 43.7 1.0 O A:HOH230 2.2 38.3 1.0 O A:HOH213 2.7 54.2 1.0 O A:HOH212 2.8 45.5 1.0 O A:HOH226 3.7 44.9 1.0 N7 A:G20 4.1 37.2 1.0 OP2 A:G20 4.2 32.2 1.0 N4 A:C22 4.3 41.0 1.0 N7 A:G21 4.5 39.4 1.0 O A:HOH221 4.5 41.1 1.0 C8 A:G20 4.6 37.8 1.0 O6 A:G21 4.7 40.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn105 b:70.8 occ:1.00 OP2 A:G36 2.1 58.6 1.0 N7 A:G37 2.2 43.1 1.0 O A:HOH216 2.4 50.5 1.0 O A:HOH221 2.4 41.1 1.0 C8 A:G37 3.1 43.9 1.0 C5 A:G37 3.3 40.8 1.0 P A:G36 3.4 63.6 1.0 OP2 A:G37 3.6 43.7 1.0 O6 A:G37 3.6 38.1 1.0 C6 A:G37 3.8 41.6 1.0 O3' A:U35 3.9 50.9 1.0 OP1 A:G36 4.1 50.5 1.0 N9 A:G37 4.3 47.3 1.0 C4 A:G37 4.4 43.5 1.0 N4 A:C38 4.5 37.7 1.0 O5' A:G36 4.5 55.1 1.0 O5' A:G37 4.7 48.4 1.0 C5' A:G36 4.8 45.0 1.0 P A:G37 4.8 45.2 1.0 O A:HOH230 4.9 38.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn106 b:76.8 occ:1.00 O A:HOH205 2.1 39.2 1.0 O A:HOH204 2.3 32.2 1.0 O A:HOH209 2.4 42.6 1.0 O6 A:G40 2.5 38.7 1.0 C6 A:G40 3.3 36.1 1.0 N7 A:G40 3.7 37.5 1.0 C5 A:G40 3.8 35.4 1.0 O6 A:G41 3.8 40.0 1.0 O4 A:U18 4.3 45.6 1.0 N7 A:G41 4.4 34.8 1.0 N4 A:C39 4.4 33.5 1.0 N1 A:G40 4.5 33.3 1.0 N6 A:A42 4.5 30.8 1.0 N4 A:C19 4.6 35.9 1.0 C6 A:G41 4.7 35.9 1.0 O4 A:U17 4.8 41.4 1.0 C8 A:G40 4.9 35.5 1.0 C5 A:G41 4.9 35.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn107 b:76.2 occ:1.00 O6 A:G27 2.0 91.2 1.0 O A:HOH203 2.3 66.0 1.0 C6 A:G27 2.3 86.5 1.0 O A:HOH202 2.4 67.8 1.0 O A:HOH207 2.4 73.9 1.0 N1 A:G27 2.9 81.2 1.0 C5 A:G27 3.0 86.7 1.0 OP1 A:A29 3.5 82.7 1.0 N7 A:G27 3.6 85.9 1.0 C2 A:G27 3.9 84.4 1.0 C4 A:G27 4.0 86.8 1.0 OP2 A:A29 4.3 89.6 1.0 P A:A29 4.4 92.3 1.0 N3 A:G27 4.5 86.2 1.0 C8 A:G27 4.7 85.0 1.0 N2 A:G27 4.8 83.6 1.0 N9 A:G27 4.9 83.5 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