Magnesium in PDB 6tfg: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps), PDB code: 6tfg 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)	47.76 / 2.45
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.530, 59.030, 191.030, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.5

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps) also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps) (pdb code 6tfg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps), PDB code: 6tfg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps)


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 3-Phosphate 5-Phosphosulfate (Apps) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:58.5 occ:1.00 O A:HOH209 2.0 64.9 1.0 OP2 A:C9 2.0 95.0 1.0 N7 A:A10 2.0 77.7 1.0 OP2 A:A8 2.0 88.6 1.0 O A:HOH210 2.1 58.5 1.0 O A:HOH211 2.3 65.0 1.0 C8 A:A10 2.9 67.1 1.0 C5 A:A10 3.1 67.5 1.0 P A:C9 3.4 80.3 1.0 P A:A8 3.4 79.9 1.0 N6 A:A10 3.5 75.2 1.0 C6 A:A10 3.7 74.0 1.0 OP1 A:C9 4.0 78.3 1.0 O5' A:A8 4.1 74.5 1.0 N9 A:A10 4.2 67.5 1.0 OP1 A:A8 4.2 99.3 1.0 O5' A:C9 4.2 72.2 1.0 C4 A:A10 4.2 60.5 1.0 C5' A:A8 4.3 79.4 1.0 OP2 A:C14 4.3 70.0 1.0 O3' A:A8 4.4 83.8 1.0 OP2 A:C15 4.4 71.3 1.0 O3' A:A7 4.5 74.9 1.0 O A:HOH207 4.5 66.0 1.0 C5 A:C9 4.5 86.2 1.0 C3' A:A8 4.7 79.7 1.0 C6 A:C9 4.9 82.0 1.0 C5 A:C15 4.9 68.0 1.0 O A:HOH215 5.0 75.2 1.0 MG A:MG106 5.0 69.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps)


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 3-Phosphate 5-Phosphosulfate (Apps) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:65.6 occ:1.00 O A:HOH201 1.9 53.3 1.0 OP1 A:U17 2.2 78.3 1.0 P A:U17 3.6 68.7 1.0 OP2 A:U17 4.3 74.7 1.0 O3' A:G16 4.4 69.5 1.0 O5' A:U17 4.7 71.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps)


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 3-Phosphate 5-Phosphosulfate (Apps) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:81.9 occ:1.00 O A:HOH205 2.0 87.7 1.0 O A:HOH208 2.2 74.5 1.0 O A:HOH217 2.2 80.5 1.0 O A:HOH216 2.3 74.5 1.0 N7 A:G38 3.8 68.8 1.0 O2' A:G36 4.0 85.0 1.0 O6 A:G38 4.3 67.3 1.0 C2' A:G36 4.6 77.4 1.0 C5 A:G38 4.7 64.5 1.0 C8 A:G38 4.7 65.5 1.0 C4 A:G36 4.9 61.1 1.0 C6 A:G38 4.9 61.9 1.0 N9 A:G36 4.9 63.5 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps)


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 3-Phosphate 5-Phosphosulfate (Apps) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:80.0 occ:1.00 O A:HOH203 2.1 72.6 1.0 O A:HOH202 2.2 74.8 1.0 O A:HOH213 2.3 68.9 1.0 O6 A:G47 2.5 92.3 1.0 O A:HOH214 2.7 89.2 1.0 C6 A:G47 3.4 86.0 1.0 N7 A:G47 3.8 82.2 1.0 C5 A:G47 3.9 84.2 1.0 O6 A:G48 4.1 90.7 1.0 N7 A:G48 4.1 96.4 1.0 O4 A:U46 4.4 90.7 1.0 N4 A:C6 4.4 77.0 1.0 N1 A:G47 4.5 81.0 1.0 O4 A:U5 4.8 86.5 1.0 N6 A:A49 4.8 98.0 1.0 C6 A:G48 4.8 88.8 1.0 C5 A:G48 4.9 93.5 1.0 C4 A:U46 4.9 84.4 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps)


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 3-Phosphate 5-Phosphosulfate (Apps) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:79.7 occ:1.00 O6 A:G20 2.9 85.2 1.0 O6 A:G19 3.0 87.3 1.0 O4 A:U41 3.5 65.0 1.0 N7 A:G20 3.8 86.9 1.0 C6 A:G20 3.9 79.7 1.0 C6 A:G19 3.9 86.7 1.0 N4 A:C42 4.0 66.0 1.0 C5 A:G20 4.2 79.2 1.0 C4 A:U41 4.5 67.0 1.0 O4 A:U21 4.5 88.3 1.0 N3 A:U41 4.6 73.2 1.0 C5 A:G19 4.6 85.9 1.0 N6 A:A40 4.7 78.1 1.0 N7 A:G19 4.8 81.0 1.0 N1 A:G19 4.8 87.3 1.0 C4 A:C42 4.9 81.3 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 3-Phosphate 5-Phosphosulfate (Apps)


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 3-Phosphate 5-Phosphosulfate (Apps) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:69.3 occ:1.00 OP1 A:A8 1.6 99.3 1.0 O5P A:PPS112 2.0 99.0 1.0 O A:HOH215 2.0 75.2 1.0 O A:HOH204 2.1 61.4 1.0 O A:HOH207 2.3 66.0 1.0 O A:HOH206 2.4 59.7 1.0 P A:A8 3.0 79.9 1.0 P2 A:PPS112 3.2 0.1 1.0 O6P A:PPS112 3.3 0.1 1.0 O A:HOH211 3.6 65.0 1.0 O5' A:A8 3.7 74.5 1.0 C5' A:A8 3.8 79.4 1.0 OP2 A:A8 3.8 88.6 1.0 OP2 A:C15 4.1 71.3 1.0 C5' A:A7 4.1 68.0 1.0 O3' A:A7 4.1 74.9 1.0 C3' A:A7 4.1 68.6 1.0 O4P A:PPS112 4.2 0.0 1.0 C4' A:A7 4.2 72.3 1.0 O5' A:PPS112 4.3 0.2 1.0 OP1 A:C15 4.5 69.8 1.0 OP1 A:C14 4.6 73.5 1.0 OP1 A:A7 4.6 80.7 1.0 O A:HOH210 4.7 58.5 1.0 S2 A:PPS112 4.7 0.6 1.0 P A:C15 4.8 68.5 1.0 OS1 A:PPS112 4.9 0.4 1.0 O5' A:A7 5.0 73.0 1.0 MG A:MG101 5.0 58.5 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