Magnesium in PDB 7d7w: Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)

The structure of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), PDB code: 7d7w 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)	25.03 / 2.39
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.392, 57.442, 196.444, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 23.6

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

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) (pdb code 7d7w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), PDB code: 7d7w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:73.4 occ:1.00 OP2 A:A8 1.9 70.2 1.0 N7 A:A10 2.0 74.8 1.0 OP2 A:C9 2.0 74.6 1.0 O A:HOH211 2.0 65.3 1.0 O A:HOH213 2.2 73.8 1.0 O A:HOH203 2.3 71.9 1.0 C8 A:A10 2.9 71.9 1.0 C5 A:A10 3.1 73.0 1.0 P A:A8 3.3 78.5 1.0 P A:C9 3.4 75.6 1.0 N6 A:A10 3.5 73.7 1.0 C6 A:A10 3.7 74.9 1.0 O5' A:A8 4.0 80.1 1.0 N9 A:A10 4.1 73.0 1.0 OP1 A:A8 4.1 74.8 1.0 C4 A:A10 4.2 76.0 1.0 O5' A:C9 4.2 76.5 1.0 C5' A:A8 4.3 79.5 1.0 OP2 A:C14 4.3 77.2 1.0 O3' A:A7 4.3 76.1 1.0 O3' A:A8 4.3 78.1 1.0 OP1 A:C9 4.3 77.3 1.0 C5 A:C9 4.4 72.3 1.0 OP2 A:C15 4.4 74.1 1.0 O A:HOH206 4.5 73.3 1.0 C3' A:A8 4.5 72.1 1.0 C6 A:C9 4.7 74.2 1.0 C4' A:A8 5.0 77.5 1.0

Magnesium binding site 2 out of 11 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:75.9 occ:1.00 O A:HOH221 2.0 76.2 1.0 O2A A:NAD102 2.2 85.8 1.0 OP1 A:A8 2.2 74.8 1.0 O A:HOH206 2.4 73.3 1.0 O A:HOH205 2.4 70.4 1.0 O1N A:NAD102 2.7 0.3 1.0 O3 A:NAD102 2.9 97.6 1.0 PA A:NAD102 3.1 93.5 1.0 O5D A:NAD102 3.1 0.2 1.0 PN A:NAD102 3.2 0.0 1.0 P A:A8 3.4 78.5 1.0 O A:HOH213 3.5 73.8 1.0 C5' A:A8 3.7 79.5 1.0 O5' A:A8 3.9 80.1 1.0 OP2 A:A8 4.0 70.2 1.0 O1A A:NAD102 4.1 97.6 1.0 OP1 A:C14 4.2 85.3 1.0 O5B A:NAD102 4.2 86.4 1.0 C5D A:NAD102 4.5 0.5 1.0 OP2 A:C15 4.6 74.1 1.0 O2N A:NAD102 4.7 0.1 1.0 O3' A:A7 4.7 76.1 1.0 O4D A:NAD102 4.7 0.7 1.0 C3' A:A7 4.9 73.0 1.0 C5' A:A7 4.9 78.5 1.0 O A:HOH203 4.9 71.9 1.0 C4' A:A7 5.0 76.6 1.0

Magnesium binding site 3 out of 11 in the Crystal Structure of the DOMAIN1 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 DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:71.5 occ:1.00 OP1 A:U17 2.1 68.0 1.0 P A:U17 3.4 71.3 1.0 O3' A:G16 3.7 70.9 1.0 OP2 A:U17 4.3 72.9 1.0 O5' A:U17 4.5 71.6 1.0 C5' A:U17 4.5 68.0 1.0 C2 A:A10 5.0 71.9 1.0

Magnesium binding site 4 out of 11 in the Crystal Structure of the DOMAIN1 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 4 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:84.1 occ:1.00 O A:HOH234 2.3 73.2 1.0 O A:HOH210 2.3 73.7 1.0 O A:HOH229 2.5 79.6 1.0 O A:HOH216 2.6 75.5 1.0 O A:HOH223 2.8 75.7 1.0 N7 A:G38 3.7 77.6 1.0 O A:HOH239 4.4 85.1 1.0 C8 A:G38 4.4 78.7 1.0 C5 A:G38 4.5 77.8 1.0 O2' A:G36 4.5 82.0 1.0 O6 A:G38 4.5 81.4 1.0 C6 A:G38 4.8 79.0 1.0 OP2 A:G38 4.8 81.6 1.0 O A:HOH231 4.9 84.6 1.0

Magnesium binding site 5 out of 11 in the Crystal Structure of the DOMAIN1 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 5 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:85.0 occ:1.00 O A:HOH231 2.0 84.6 1.0 O A:HOH239 2.3 85.1 1.0 O A:HOH243 2.5 92.2 1.0 O A:HOH208 2.7 83.8 1.0 C5 A:C12 3.7 79.7 1.0 N4 A:C12 4.0 78.6 1.0 C4 A:C12 4.3 76.5 1.0 O A:HOH216 4.7 75.5 1.0 C6 A:C12 4.7 82.0 1.0 N4 A:C13 4.7 76.8 1.0 OP1 A:C12 4.8 80.0 1.0 OP2 A:C12 4.9 81.9 1.0

Magnesium binding site 6 out of 11 in the Crystal Structure of the DOMAIN1 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 6 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:74.4 occ:1.00 O A:HOH233 2.0 75.9 1.0 O A:HOH207 2.3 64.9 1.0 O6 A:G47 2.3 74.0 1.0 O A:HOH212 2.4 67.9 1.0 O A:HOH201 2.7 62.7 1.0 O A:HOH230 2.7 74.1 1.0 N7 A:G47 2.9 70.8 1.0 C6 A:G47 3.1 72.8 1.0 C5 A:G47 3.3 72.8 1.0 O4 A:U46 3.5 76.8 1.0 C4 A:U46 3.7 78.8 1.0 C5 A:U46 3.8 81.9 1.0 C8 A:G47 4.1 71.9 1.0 N1 A:G47 4.4 70.6 1.0 C4 A:G47 4.6 75.2 1.0 N3 A:U46 4.6 76.9 1.0 N7 A:G48 4.7 71.9 1.0 C6 A:U46 4.7 79.4 1.0 N4 A:C6 4.8 61.8 1.0

Magnesium binding site 7 out of 11 in the Crystal Structure of the DOMAIN1 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 7 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:85.7 occ:1.00 O A:HOH226 2.1 83.8 1.0 O A:HOH202 2.3 76.1 1.0 O A:HOH219 2.3 85.0 1.0 O A:HOH214 2.4 83.3 1.0 O A:HOH222 2.5 81.6 1.0 OP2 A:A7 2.6 77.5 1.0 OP1 A:G16 3.5 76.5 1.0 P A:A7 3.8 80.0 1.0 O5' A:A7 3.8 75.4 1.0 C8 A:A7 3.9 73.9 1.0 OP2 A:G16 4.0 73.9 1.0 P A:G16 4.2 75.5 1.0 C2' A:A7 4.3 73.6 1.0 N7 A:A7 4.4 72.7 1.0 OP1 A:C15 4.5 78.8 1.0 OP1 A:A7 4.7 75.8 1.0 N9 A:A7 4.7 68.3 1.0 O2' A:A7 4.7 75.7 1.0 O3' A:C6 5.0 78.6 1.0

Magnesium binding site 8 out of 11 in the Crystal Structure of the DOMAIN1 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 8 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:87.6 occ:1.00 O A:HOH235 2.2 76.1 1.0 O A:HOH227 2.2 84.4 1.0 O A:HOH240 2.3 84.5 1.0 O A:HOH220 2.6 72.9 1.0 O2 A:C9 3.6 76.3 1.0 O A:HOH217 3.8 68.7 1.0 N1 A:A8 4.4 74.5 1.0 C2 A:C9 4.6 75.2 1.0

Magnesium binding site 9 out of 11 in the Crystal Structure of the DOMAIN1 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 9 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:86.3 occ:1.00 O A:HOH215 2.3 90.8 1.0 O A:HOH228 2.4 90.6 1.0 O A:HOH236 2.4 83.5 1.0 O A:HOH224 2.5 84.7 1.0 N7 A:G28 3.2 81.1 1.0 OP2 A:A30 3.3 83.5 1.0 C8 A:G28 3.7 83.1 1.0 C5 A:G28 3.8 78.8 1.0 P A:A30 3.9 86.8 1.0 OP1 A:A30 3.9 89.3 1.0 O6 A:G28 4.3 83.9 1.0 O3' A:A29 4.3 87.6 1.0 C6 A:G28 4.3 81.6 1.0 C5' A:A29 4.3 78.0 1.0 N9 A:G28 4.6 83.2 1.0 C4 A:G28 4.7 80.4 1.0 O5' A:A29 4.7 80.2 1.0 OP2 A:A29 4.9 84.6 1.0 C3' A:A29 5.0 83.0 1.0

Magnesium binding site 10 out of 11 in the Crystal Structure of the DOMAIN1 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 10 of Crystal Structure of the DOMAIN1 of Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg112 b:0.3 occ:1.00 O2A A:GTP101 2.5 0.7 1.0 O2B A:GTP101 2.7 0.4 1.0 PB A:GTP101 3.7 1.0 1.0 O3B A:GTP101 3.7 0.7 1.0 PA A:GTP101 3.9 0.2 1.0 O3A A:GTP101 4.3 0.3 1.0 O5' A:GTP101 4.6 0.1 1.0 O1A A:GTP101 4.9 0.9 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