Magnesium in PDB 6tf3: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp), PDB code: 6tf3 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)	55.09 / 2.66
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.530, 58.150, 191.140, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.1

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp) also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp) (pdb code 6tf3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp), PDB code: 6tf3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp)


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 Cordycepin 5-Triphosphate (3-Datp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:70.5 occ:1.00 O3B A:3AT109 2.2 0.9 1.0 OP1 A:A8 2.5 75.3 1.0 O2A A:3AT109 2.9 96.3 1.0 O1A A:3AT109 3.4 0.5 1.0 PB A:3AT109 3.5 0.1 1.0 PA A:3AT109 3.6 96.1 1.0 OP2 A:C15 3.9 78.9 1.0 O3A A:3AT109 4.0 98.0 1.0 P A:A8 4.0 78.2 1.0 OP1 A:C14 4.0 74.0 1.0 O2B A:3AT109 4.1 0.0 1.0 OP1 A:A7 4.2 86.1 1.0 OP1 A:C15 4.4 77.0 1.0 C5' A:A7 4.6 79.6 1.0 O5' A:A8 4.6 80.6 1.0 P A:C15 4.6 71.0 1.0 OP2 A:A8 4.7 87.9 1.0 C5' A:A8 4.8 77.9 1.0 O1B A:3AT109 4.8 0.4 1.0 C3' A:A7 4.9 66.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp)


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 Cordycepin 5-Triphosphate (3-Datp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:58.7 occ:1.00 N7 A:A10 2.0 76.6 1.0 OP2 A:C9 2.0 90.5 1.0 OP2 A:A8 2.0 87.9 1.0 C8 A:A10 3.0 68.1 1.0 C5 A:A10 3.0 62.3 1.0 N6 A:A10 3.3 92.0 1.0 P A:A8 3.4 78.2 1.0 P A:C9 3.4 83.9 1.0 C6 A:A10 3.6 81.1 1.0 OP2 A:C14 3.9 74.0 1.0 N9 A:A10 4.2 68.4 1.0 OP1 A:A8 4.2 75.3 1.0 C4 A:A10 4.2 61.3 1.0 OP1 A:C9 4.2 89.5 1.0 OP2 A:C15 4.2 78.9 1.0 O5' A:C9 4.3 69.7 1.0 O5' A:A8 4.3 80.6 1.0 O3' A:A8 4.4 91.4 1.0 C5' A:A8 4.4 77.9 1.0 O3' A:A7 4.4 69.8 1.0 C3' A:A8 4.6 86.9 1.0 C5 A:C9 4.7 81.5 1.0 N1 A:A10 4.9 65.9 1.0 P A:C14 5.0 73.1 1.0 C5 A:C15 5.0 64.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp)


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 Cordycepin 5-Triphosphate (3-Datp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:59.3 occ:1.00 OP1 A:U17 2.2 57.6 1.0 P A:U17 3.6 71.6 1.0 C5' A:U17 3.8 58.9 1.0 O3' A:G16 4.1 59.4 1.0 O5' A:U17 4.2 70.3 1.0 OP2 A:U17 4.8 71.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Cordycepin 5-Triphosphate (3-Datp)


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 Cordycepin 5-Triphosphate (3-Datp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:92.4 occ:1.00 N7 A:G38 3.6 60.2 1.0 O2' A:G36 4.1 87.6 1.0 O6 A:G38 4.4 68.9 1.0 C8 A:G38 4.4 63.4 1.0 C5 A:G38 4.5 60.2 1.0 C6 A:G38 4.8 62.8 1.0 C2' A:G36 4.8 80.8 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