Magnesium in PDB 6tf1: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Adenosine Diphosphate (Adp), PDB code: 6tf1 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)	56.37 / 2.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.585, 59.014, 190.587, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.5

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

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 Diphosphate (Adp) (pdb code 6tf1). 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 Diphosphate (Adp), PDB code: 6tf1:
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 Diphosphate (Adp)


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:59.1 occ:1.00 O A:HOH205 1.9 53.7 1.0 OP1 A:U17 1.9 83.4 1.0 O A:HOH215 1.9 66.4 1.0 P A:U17 3.4 60.7 1.0 O3' A:G16 4.0 54.6 1.0 OP2 A:U17 4.2 65.0 1.0 O5' A:U17 4.4 58.9 1.0 C5' A:U17 4.6 62.7 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:52.1 occ:1.00 O A:HOH206 1.9 58.2 1.0 OP2 A:A8 2.0 80.3 1.0 O A:HOH202 2.0 56.1 1.0 OP2 A:C9 2.0 80.7 1.0 N7 A:A10 2.1 67.7 1.0 O A:HOH203 2.2 73.1 1.0 C8 A:A10 3.1 56.5 1.0 C5 A:A10 3.1 57.6 1.0 N6 A:A10 3.3 72.4 1.0 P A:A8 3.4 69.2 1.0 P A:C9 3.4 74.4 1.0 C6 A:A10 3.6 63.2 1.0 O5' A:A8 4.0 66.1 1.0 OP2 A:C14 4.1 73.6 1.0 N9 A:A10 4.2 60.7 1.0 OP1 A:C9 4.2 73.0 1.0 C5' A:A8 4.2 74.7 1.0 C4 A:A10 4.2 51.9 1.0 OP1 A:A8 4.2 83.5 1.0 O5' A:C9 4.3 67.4 1.0 O A:HOH210 4.3 75.0 1.0 O3' A:A7 4.4 61.3 1.0 OP2 A:C15 4.4 69.6 1.0 O3' A:A8 4.4 76.8 1.0 C3' A:A8 4.6 76.1 1.0 C5 A:C9 4.7 62.3 1.0 C5 A:C15 5.0 63.9 1.0 N1 A:A10 5.0 51.1 1.0 C6 A:C9 5.0 69.4 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:71.5 occ:1.00 O6 A:G47 2.3 98.2 1.0 C6 A:G47 3.1 86.9 1.0 N7 A:G47 3.6 79.1 1.0 C5 A:G47 3.7 77.2 1.0 O6 A:G48 3.7 72.6 1.0 N7 A:G48 4.0 75.4 1.0 O4 A:U46 4.2 85.9 1.0 N1 A:G47 4.4 80.6 1.0 N4 A:C6 4.5 62.7 1.0 O4 A:U5 4.5 79.7 1.0 C6 A:G48 4.6 74.6 1.0 C5 A:G48 4.7 74.8 1.0 C4 A:U46 4.8 81.0 1.0 C8 A:G47 4.9 73.3 1.0 N6 A:A49 4.9 70.4 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:74.8 occ:1.00 O A:HOH218 2.3 63.0 1.0 O A:HOH212 2.4 62.6 1.0 O A:HOH214 2.4 61.5 1.0 O A:HOH216 2.4 71.7 1.0 N7 A:G38 4.5 51.0 1.0 O2' A:G36 4.7 80.9 1.0 O6 A:G38 4.9 62.2 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:80.1 occ:1.00 O6 A:G19 3.0 80.9 1.0 O6 A:G20 3.1 72.7 1.0 O4 A:U41 3.6 70.8 1.0 C6 A:G19 3.9 73.3 1.0 N7 A:G20 4.2 71.1 1.0 C6 A:G20 4.2 68.1 1.0 N4 A:C42 4.4 51.0 1.0 C5 A:G19 4.5 69.0 1.0 C5 A:G20 4.6 65.8 1.0 N7 A:G19 4.6 71.0 1.0 C4 A:U41 4.6 64.1 1.0 N6 A:A40 4.8 72.2 1.0 N1 A:G19 4.8 69.5 1.0 O4 A:U21 4.8 74.0 1.0 N3 A:U41 4.9 66.3 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:66.6 occ:1.00 O A:HOH204 1.8 76.4 1.0 O2B A:ADP109 2.0 0.4 1.0 O A:HOH210 2.1 75.0 1.0 O A:HOH208 2.1 64.2 1.0 OP1 A:A8 2.2 83.5 1.0 O2A A:ADP109 2.6 0.8 1.0 O3A A:ADP109 3.0 0.9 1.0 PB A:ADP109 3.1 0.5 1.0 PA A:ADP109 3.4 0.4 1.0 P A:A8 3.6 69.2 1.0 O3B A:ADP109 3.8 1.0 1.0 O A:HOH202 4.0 56.1 1.0 O5' A:ADP109 4.0 96.2 1.0 C5' A:A7 4.0 72.4 1.0 O A:HOH201 4.1 61.1 1.0 OP2 A:C15 4.2 69.6 1.0 O5' A:A8 4.3 66.1 1.0 C5' A:A8 4.3 74.7 1.0 O1B A:ADP109 4.4 0.5 1.0 C4' A:A7 4.4 65.0 1.0 OP2 A:A8 4.4 80.3 1.0 OP1 A:A7 4.5 95.8 1.0 C3' A:A7 4.5 60.5 1.0 OP1 A:C14 4.5 66.6 1.0 O3' A:A7 4.6 61.3 1.0 OP1 A:C15 4.6 72.1 1.0 O1A A:ADP109 4.7 0.3 1.0 P A:C15 4.9 64.6 1.0

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


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 Diphosphate (Adp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:78.0 occ:1.00 OP2 A:A7 2.3 71.3 1.0 P A:A7 3.5 77.8 1.0 OP1 A:C15 3.9 72.1 1.0 OP1 A:G16 4.0 73.4 1.0 O5' A:A7 4.0 76.1 1.0 OP1 A:A7 4.1 95.8 1.0 OP2 A:G16 4.1 49.6 1.0 P A:G16 4.5 65.0 1.0 C5' A:C15 4.5 51.8 1.0 C8 A:A7 4.6 70.0 1.0 C2' A:A7 4.6 57.8 1.0 O3' A:C6 4.9 78.8 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