Magnesium in PDB 6tf2: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 5-Triphosphate (Atp)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 5-Triphosphate (Atp), PDB code: 6tf2 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)	54.98 / 2.55
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.410, 59.030, 190.980, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 23.9

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

Bromine	(Br)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 5-Triphosphate (Atp) (pdb code 6tf2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 5-Triphosphate (Atp), PDB code: 6tf2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 5-Triphosphate (Atp)


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 5-Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:70.7 occ:1.00 OP2 A:A8 2.0 76.8 1.0 OP2 A:C9 2.0 78.2 1.0 N7 A:A10 2.3 61.1 1.0 P A:A8 3.3 76.2 1.0 C5 A:A10 3.3 63.7 1.0 C8 A:A10 3.3 64.9 1.0 N6 A:A10 3.4 88.8 1.0 P A:C9 3.4 75.5 1.0 C6 A:A10 3.8 78.4 1.0 OP1 A:A8 3.9 62.0 1.0 OP2 A:C14 3.9 70.8 1.0 O5' A:A8 4.0 80.2 1.0 OP1 A:C9 4.0 78.5 1.0 C5' A:A8 4.0 81.7 1.0 O3' A:A8 4.3 84.0 1.0 OP2 A:C15 4.3 83.2 1.0 O5' A:C9 4.4 69.7 1.0 C3' A:A8 4.5 80.0 1.0 O3' A:A7 4.5 65.8 1.0 C4 A:A10 4.5 59.4 1.0 O1B A:ATP109 4.5 0.3 1.0 N9 A:A10 4.5 65.6 1.0 C4' A:A8 4.8 81.0 1.0 P A:C14 4.8 69.7 1.0 OP1 A:C14 4.8 73.9 1.0 MG A:MG105 4.9 92.2 1.0 C5 A:C9 4.9 83.9 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 5-Triphosphate (Atp)


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 5-Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:58.9 occ:1.00 O A:HOH201 2.0 54.2 1.0 OP1 A:U17 2.2 73.5 1.0 P A:U17 3.5 69.4 1.0 O3' A:G16 3.9 55.8 1.0 C5' A:U17 4.0 58.3 1.0 O5' A:U17 4.2 58.3 1.0 OP2 A:U17 4.8 73.7 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 5-Triphosphate (Atp)


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 5-Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:84.1 occ:1.00 O A:HOH204 2.2 69.8 1.0 N7 A:G38 3.4 73.5 1.0 O6 A:G38 4.0 70.9 1.0 O2' A:G36 4.1 82.5 1.0 C5 A:G38 4.2 62.9 1.0 C8 A:G38 4.3 66.4 1.0 C6 A:G38 4.4 63.9 1.0 C2' A:G36 5.0 71.3 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine 5-Triphosphate (Atp)


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 5-Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:0.1 occ:1.00 O A:HOH202 2.4 80.7 1.0 O6 A:G47 2.6 96.7 1.0 N7 A:G47 3.2 82.9 1.0 C6 A:G47 3.3 87.9 1.0 C5 A:G47 3.6 83.5 1.0 O4 A:U46 3.8 87.4 1.0 C4 A:U46 4.2 82.9 1.0 C8 A:G47 4.4 77.9 1.0 C5 A:U46 4.5 83.4 1.0 N7 A:G48 4.6 86.3 1.0 N1 A:G47 4.7 79.8 1.0 C4 A:G47 4.9 74.7 1.0 O6 A:G48 4.9 96.4 1.0 N4 A:C6 5.0 69.1 1.0

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


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 5-Triphosphate (Atp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:92.2 occ:1.00 O A:HOH203 2.0 84.2 1.0 O1A A:ATP109 2.0 0.6 1.0 O1G A:ATP109 2.3 0.1 1.0 OP1 A:A8 2.5 62.0 1.0 O1B A:ATP109 2.6 0.3 1.0 PA A:ATP109 3.5 0.4 1.0 OP1 A:C14 3.7 73.9 1.0 PG A:ATP109 3.7 0.8 1.0 PB A:ATP109 3.8 0.7 1.0 OP2 A:C15 3.8 83.2 1.0 P A:A8 3.9 76.2 1.0 O3A A:ATP109 4.1 0.2 1.0 O3B A:ATP109 4.2 0.1 1.0 O3G A:ATP109 4.4 0.0 1.0 O5' A:ATP109 4.4 0.3 1.0 O2A A:ATP109 4.5 0.9 1.0 OP2 A:A8 4.5 76.8 1.0 OP1 A:C15 4.5 74.5 1.0 O5' A:A8 4.6 80.2 1.0 C5' A:A8 4.6 81.7 1.0 P A:C15 4.7 69.6 1.0 C5' A:A7 4.8 74.0 1.0 O2G A:ATP109 4.8 0.2 1.0 MG A:MG101 4.9 70.7 1.0 OP1 A:A7 4.9 79.0 1.0 P A:C14 4.9 69.7 1.0 C3' A:A7 5.0 68.0 1.0 O3' A:A7 5.0 65.8 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