Manganese in PDB 7d7z: Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+

The structure of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+, PDB code: 7d7z 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)	30.00 / 2.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.804, 57.318, 196.564, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.4

The structure of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ also contains other interesting chemical elements:

Magnesium

(Mg)

11 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ (pdb code 7d7z). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+, PDB code: 7d7z:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn113 b:76.5 occ:1.00 O A:HOH277 2.0 65.7 1.0 O A:HOH206 2.1 58.1 1.0 N7 A:G32 2.3 56.4 1.0 O A:HOH232 2.4 60.1 1.0 O A:HOH210 2.5 61.1 1.0 O A:HOH266 2.7 63.2 1.0 C8 A:G32 3.1 55.2 1.0 C5 A:G32 3.5 55.3 1.0 OP2 A:A31 3.8 61.5 1.0 O A:HOH285 3.8 67.7 1.0 O6 A:G32 4.0 55.4 1.0 C6 A:G32 4.1 54.5 1.0 N9 A:G32 4.4 56.7 1.0 OP2 A:G32 4.4 64.2 1.0 C4 A:G32 4.6 55.8 1.0 O A:HOH289 4.6 67.2 1.0 N2 A:G28 4.7 57.1 1.0 P A:A31 4.7 64.0 1.0 O A:HOH288 4.9 64.9 1.0 OP1 A:A31 4.9 66.0 1.0 N1 A:G28 4.9 55.4 1.0

Manganese binding site 2 out of 16 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn114 b:59.4 occ:1.00 O A:HOH237 2.0 52.6 1.0 OP2 A:G25 2.2 56.0 1.0 O A:HOH258 2.3 44.7 1.0 O A:HOH242 2.3 44.2 1.0 O A:HOH245 2.4 56.2 1.0 O A:HOH259 2.4 51.4 1.0 P A:G25 3.5 58.5 1.0 O5' A:G25 3.9 49.6 1.0 N7 A:G25 4.0 56.6 1.0 C8 A:G25 4.1 56.0 1.0 O A:HOH280 4.5 57.6 1.0 OP1 A:G25 4.5 67.1 1.0 O3' A:G24 4.5 60.2 1.0 N7 A:A26 4.6 56.4 1.0 C3' A:G24 4.6 57.3 1.0 OP2 A:A26 4.7 52.7 1.0 N6 A:A26 4.8 51.7 1.0 C5 A:G25 4.9 54.2 1.0

Manganese binding site 3 out of 16 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn115 b:70.5 occ:1.00 O A:HOH220 2.4 50.0 1.0 O A:HOH287 2.4 47.7 1.0 O A:HOH234 2.5 56.1 1.0 O A:HOH251 2.5 58.6 1.0 O A:HOH289 2.6 67.2 1.0 O A:HOH280 2.7 57.6 1.0 O6 A:G25 3.4 54.3 1.0 O6 A:G24 4.1 51.7 1.0 O4 A:U33 4.2 57.9 1.0 N7 A:G24 4.2 50.8 1.0 O A:HOH245 4.3 56.2 1.0 O A:HOH232 4.3 60.1 1.0 O A:HOH288 4.4 64.9 1.0 N4 A:C34 4.5 52.5 1.0 C6 A:G25 4.5 53.8 1.0 O A:HOH277 4.6 65.7 1.0 C6 A:G24 4.7 51.6 1.0 O A:HOH223 4.7 53.5 1.0 C5 A:G24 4.7 52.1 1.0 O A:HOH242 4.8 44.2 1.0 N7 A:G25 4.9 56.6 1.0 MG A:MG110 4.9 56.6 1.0 O A:HOH282 4.9 64.1 1.0 N6 A:A26 4.9 51.7 1.0

Manganese binding site 4 out of 16 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn116 b:56.2 occ:1.00 O A:HOH279 2.0 47.8 1.0 O A:HOH223 2.1 53.5 1.0 O A:HOH263 2.2 54.2 1.0 N7 A:G23 2.3 54.7 1.0 O A:HOH236 2.5 58.9 1.0 O A:HOH282 2.6 64.1 1.0 O A:HOH262 3.0 51.9 1.0 C8 A:G23 3.0 56.2 1.0 C5 A:G23 3.4 52.9 1.0 O6 A:G23 3.9 52.1 1.0 N7 A:G22 4.1 54.2 1.0 C6 A:G23 4.1 52.1 1.0 O A:HOH220 4.2 50.0 1.0 N9 A:G23 4.3 54.2 1.0 C8 A:G22 4.4 55.6 1.0 OP2 A:G23 4.4 61.4 1.0 C4 A:G23 4.5 53.5 1.0 C5 A:G22 4.8 54.2 1.0 OP2 A:G22 4.9 65.4 1.0 O A:HOH287 4.9 47.7 1.0

Manganese binding site 5 out of 16 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn117 b:90.7 occ:1.00 O A:HOH250 2.0 59.6 1.0 O A:HOH219 2.4 68.8 1.0 O A:HOH226 2.4 64.4 1.0 O A:HOH281 2.6 65.8 1.0 O A:HOH214 2.8 61.3 1.0 N7 A:G20 2.8 61.2 1.0 C8 A:G20 3.7 62.9 1.0 N7 A:G19 3.9 64.7 1.0 C5 A:G20 3.9 60.8 1.0 O6 A:G20 4.1 60.3 1.0 C5 A:G19 4.2 62.5 1.0 C8 A:G19 4.4 62.2 1.0 C6 A:G20 4.4 60.6 1.0 OP2 A:G20 4.4 72.4 1.0 C6 A:G19 4.5 58.5 1.0 O6 A:G19 4.6 58.3 1.0 O4 A:U21 4.9 57.5 1.0 C4 A:G19 4.9 62.0 1.0 N9 A:G20 5.0 63.3 1.0 MG A:MG105 5.0 69.8 1.0

Manganese binding site 6 out of 16 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn118 b:64.4 occ:1.00 OP2 A:A7 2.2 51.6 1.0 O A:HOH255 2.3 49.0 1.0 O A:HOH243 2.3 48.3 1.0 O A:HOH231 2.4 48.8 1.0 O A:HOH274 2.5 62.8 1.0 O A:HOH204 2.5 52.8 1.0 P A:A7 3.4 59.0 1.0 O5' A:A7 3.9 51.2 1.0 OP1 A:A7 4.3 51.9 1.0 OP1 A:G16 4.3 51.1 1.0 OP1 A:C15 4.4 54.0 1.0 OP2 A:G16 4.6 49.4 1.0 O A:HOH244 4.7 45.6 1.0 O3' A:C6 4.7 59.8 1.0 C8 A:A7 4.8 47.4 1.0 C2' A:A7 4.9 52.1 1.0 P A:G16 4.9 46.8 1.0 C3' A:C6 4.9 55.2 1.0

Manganese binding site 7 out of 16 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn119 b:61.5 occ:1.00 O A:HOH271 2.0 44.4 1.0 O A:HOH207 2.4 46.4 1.0 O A:HOH209 2.5 45.7 1.0 O A:HOH264 2.6 45.9 1.0 O6 A:G47 2.6 49.8 1.0 O A:HOH208 2.6 38.6 1.0 N7 A:G47 3.2 51.7 1.0 C6 A:G47 3.4 48.3 1.0 C5 A:G47 3.6 50.2 1.0 O4 A:U46 3.8 54.8 1.0 C4 A:U46 4.1 54.2 1.0 C5 A:U46 4.3 55.6 1.0 C8 A:G47 4.5 52.8 1.0 N4 A:C6 4.5 37.5 1.0 N7 A:G48 4.6 45.7 1.0 N1 A:G47 4.7 47.5 1.0 C4 A:G47 4.9 50.1 1.0 N3 A:U46 5.0 52.5 1.0

Manganese binding site 8 out of 16 in the Crystal Structure of the DOMAIN1 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 8 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn120 b:68.2 occ:1.00 O A:HOH239 2.2 50.9 1.0 O A:HOH224 2.2 55.1 1.0 N7 A:G36 2.4 51.5 1.0 O A:HOH269 2.4 56.1 1.0 O A:HOH278 2.6 54.1 1.0 C8 A:G36 3.3 49.7 1.0 C5 A:G36 3.6 51.1 1.0 O6 A:G36 3.9 52.5 1.0 C6 A:G36 4.1 51.2 1.0 O A:HOH273 4.3 54.5 1.0 N9 A:G36 4.5 50.5 1.0 O A:HOH257 4.6 51.8 1.0 O A:HOH260 4.7 53.5 1.0 C4 A:G36 4.7 49.2 1.0

Manganese binding site 9 out of 16 in the Crystal Structure of the DOMAIN1 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 9 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn121 b:67.7 occ:1.00 O A:HOH273 2.4 54.5 1.0 O A:HOH222 2.4 53.2 1.0 O A:HOH270 2.4 53.5 1.0 O A:HOH216 2.5 46.2 1.0 N7 A:G38 4.1 46.9 1.0 O2' A:G36 4.4 56.3 1.0 O6 A:G38 4.4 49.7 1.0 O A:HOH224 4.6 55.1 1.0 C5 A:G38 4.9 46.8 1.0 C8 A:G38 5.0 48.0 1.0 C6 A:G38 5.0 49.3 1.0 C5 A:G36 5.0 51.1 1.0

Manganese binding site 10 out of 16 in the Crystal Structure of the DOMAIN1 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 10 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), Soaked in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn122 b:77.3 occ:1.00 N7A A:NAD129 2.4 50.7 1.0 C5A A:NAD129 3.3 44.9 1.0 C8A A:NAD129 3.4 53.5 1.0 N6A A:NAD129 3.4 47.8 1.0 C6A A:NAD129 3.8 47.7 1.0 O2' A:G48 4.3 51.5 1.0 N9A A:NAD129 4.5 51.6 1.0 C4A A:NAD129 4.6 50.8 1.0 O A:HOH233 4.6 39.0 1.0 C1' A:A8 4.6 49.8 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