Magnesium in PDB 6tb7: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp), PDB code: 6tb7 was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.59 / 2.53
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.430, 59.450, 190.380, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.8

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Sodium	(Na)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) (pdb code 6tb7). 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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp), PDB code: 6tb7:
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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:63.4 occ:1.00 OP1 A:U17 1.9 92.6 1.0 P A:U17 3.2 66.7 1.0 O3' A:G16 3.6 56.5 1.0 OP2 A:U17 4.0 79.7 1.0 O5' A:U17 4.3 65.6 1.0 C5' A:U17 4.5 67.5 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:73.2 occ:1.00 O A:HOH204 1.8 58.1 1.0 O A:HOH213 1.9 66.2 1.0 O A:HOH214 2.0 73.8 1.0 OP1 A:A8 2.1 95.0 1.0 O2P A:AMP101 2.1 0.3 1.0 O A:HOH202 2.2 75.8 1.0 P A:AMP101 3.5 0.7 1.0 P A:A8 3.5 78.0 1.0 O5' A:AMP101 3.9 0.7 1.0 O A:HOH211 3.9 58.9 1.0 OP2 A:C15 3.9 72.5 1.0 C5' A:A7 4.0 75.7 1.0 O3P A:AMP101 4.1 0.4 1.0 O A:HOH201 4.2 63.0 1.0 O5' A:A8 4.2 78.6 1.0 C5' A:A8 4.2 76.4 1.0 OP1 A:C15 4.2 75.7 1.0 OP2 A:A8 4.3 86.9 1.0 OP1 A:A7 4.3 0.3 1.0 C3' A:A7 4.4 64.1 1.0 C4' A:A7 4.4 71.0 1.0 OP1 A:C14 4.4 69.1 1.0 O3' A:A7 4.5 69.8 1.0 P A:C15 4.6 72.0 1.0 O1P A:AMP101 4.6 0.8 1.0 O A:HOH209 4.7 56.0 1.0 O5' A:A7 4.9 74.5 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:51.8 occ:1.00 N7 A:A10 1.9 71.3 1.0 OP2 A:A8 1.9 86.9 1.0 OP2 A:C9 1.9 93.8 1.0 O A:HOH212 2.0 66.7 1.0 O A:HOH211 2.3 58.9 1.0 O A:HOH209 2.4 56.0 1.0 C8 A:A10 2.9 64.6 1.0 C5 A:A10 2.9 62.4 1.0 N6 A:A10 3.2 75.4 1.0 P A:A8 3.3 78.0 1.0 P A:C9 3.3 82.6 1.0 C6 A:A10 3.5 78.8 1.0 O5' A:A8 4.0 78.6 1.0 C4 A:A10 4.1 56.1 1.0 N9 A:A10 4.1 68.8 1.0 O5' A:C9 4.1 76.7 1.0 OP1 A:A8 4.1 95.0 1.0 OP1 A:C9 4.1 77.4 1.0 O3' A:A7 4.3 69.8 1.0 C5' A:A8 4.3 76.4 1.0 O3' A:A8 4.3 91.0 1.0 C5 A:C9 4.4 87.6 1.0 O A:HOH202 4.4 75.8 1.0 OP2 A:C15 4.4 72.5 1.0 C3' A:A8 4.5 80.4 1.0 OP2 A:C14 4.5 61.6 1.0 C6 A:C9 4.7 86.6 1.0 N1 A:A10 4.8 73.3 1.0 C5 A:C15 4.9 65.8 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:74.4 occ:1.00 O A:HOH210 2.0 73.0 1.0 O A:HOH207 2.3 60.5 1.0 O A:HOH216 2.4 66.3 1.0 O A:HOH217 2.4 60.8 1.0 N7 A:G38 4.1 63.1 1.0 O6 A:G38 4.4 64.4 1.0 O2' A:G36 4.5 92.8 1.0 C5 A:G38 4.9 60.0 1.0 C6 A:G38 5.0 53.4 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:84.1 occ:1.00 O6 A:G47 2.4 95.6 1.0 C6 A:G47 3.3 77.8 1.0 N7 A:G47 3.6 87.4 1.0 C5 A:G47 3.7 79.8 1.0 O4 A:U46 4.2 80.0 1.0 O6 A:G48 4.2 87.4 1.0 N7 A:G48 4.2 82.0 1.0 N1 A:G47 4.5 72.2 1.0 N4 A:C6 4.6 65.8 1.0 C4 A:U46 4.7 76.6 1.0 C8 A:G47 4.8 80.6 1.0 O4 A:U5 4.9 81.3 1.0 C6 A:G48 4.9 85.5 1.0 C5 A:G48 5.0 86.8 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:89.0 occ:1.00 O6 A:G20 3.1 81.2 1.0 O6 A:G19 3.2 82.9 1.0 O4 A:U41 3.7 86.2 1.0 N7 A:G20 3.9 82.5 1.0 C6 A:G19 4.0 81.2 1.0 NA A:NA111 4.1 0.9 1.0 C6 A:G20 4.1 79.6 1.0 C5 A:G20 4.4 79.5 1.0 N4 A:C42 4.4 59.7 1.0 C5 A:G19 4.6 78.5 1.0 O4 A:U21 4.6 81.7 1.0 N7 A:G19 4.7 79.9 1.0 C4 A:U41 4.7 80.6 1.0 N6 A:A40 4.7 79.5 1.0 N3 A:U41 4.8 76.3 1.0 N1 A:G19 4.8 85.2 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp)


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 Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Monophosphate (Amp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:0.9 occ:1.00 OP2 A:A7 2.8 80.2 1.0 OP1 A:G16 3.7 72.7 1.0 OP2 A:G16 3.7 53.5 1.0 P A:A7 3.9 86.6 1.0 O5' A:A7 4.1 74.5 1.0 P A:G16 4.2 76.2 1.0 OP1 A:C15 4.4 75.7 1.0 C8 A:A7 4.4 67.2 1.0 C2' A:A7 4.6 68.3 1.0 C5' A:C15 4.6 52.8 1.0 OP1 A:A7 4.8 0.3 1.0 N7 A:A7 4.9 62.5 1.0

L.Huang, J.Wang, D.M.J.Lilley. Structure and Ligand Binding of the Adp-Binding Domain of the Nad + Riboswitch. Rna V. 26 878 2020.
ISSN: ESSN 1469-9001
PubMed: 32295864
DOI: 10.1261/RNA.074898.120