Sodium 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:

Magnesium

(Mg)

6 atoms

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 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 Sodium with other atoms in the Na 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:Na107 b:72.9 occ:1.00 O2 A:C15 2.8 55.5 1.0 N3 A:C15 2.8 61.1 1.0 O6 A:G36 3.0 79.9 1.0 C2 A:C15 3.2 62.4 1.0 C6 A:G36 3.4 68.2 1.0 C5 A:G36 3.8 60.9 1.0 C4 A:C15 4.0 63.1 1.0 N7 A:G36 4.1 64.1 1.0 N1 A:G36 4.1 62.9 1.0 N4 A:C14 4.3 72.3 1.0 N4 A:C15 4.4 57.4 1.0 N1 A:C15 4.6 64.7 1.0 C4 A:G36 4.8 61.1 1.0 N3 A:A10 4.9 56.7 1.0

Sodium binding site 2 out of 5 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 Sodium with other atoms in the Na 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:Na108 b:95.2 occ:1.00 OP2 A:A7 2.5 76.9 1.0 P A:A7 3.6 83.3 1.0 OP1 A:G16 3.7 79.8 1.0 O5' A:A7 3.8 73.0 1.0 OP2 A:G16 4.0 57.5 1.0 OP1 A:C15 4.1 69.8 1.0 P A:G16 4.3 69.1 1.0 OP1 A:A7 4.4 80.7 1.0 C8 A:A7 4.5 76.7 1.0 C2' A:A7 4.5 63.0 1.0 C5' A:C15 4.6 60.5 1.0 O2' A:A7 4.9 62.3 1.0 N7 A:A7 4.9 69.9 1.0 O3' A:C6 5.0 87.7 1.0

Sodium binding site 3 out of 5 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 Sodium with other atoms in the Na 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:Na109 b:99.3 occ:1.00 O6 A:G23 3.3 75.6 1.0 N7 A:G23 4.0 81.3 1.0 O4 A:U22 4.2 89.3 1.0 C6 A:G23 4.2 80.9 1.0 C5 A:U22 4.4 79.8 1.0 C5 A:G23 4.5 82.3 1.0 C4 A:U22 4.6 87.0 1.0 N4 A:C37 4.9 72.0 1.0

Sodium binding site 4 out of 5 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 Sodium with other atoms in the Na 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:Na110 b:77.9 occ:1.00 OP1 A:C37 3.7 83.2 1.0 N7 A:A35 4.1 91.0 1.0 C5 A:C37 4.2 70.7 1.0 C5 A:A35 4.2 86.6 1.0 O2' A:A35 4.2 94.9 1.0 C8 A:A35 4.2 91.1 1.0 C4 A:A35 4.5 85.4 1.0 N9 A:A35 4.5 90.4 1.0 C6 A:C37 4.6 72.4 1.0 C6 A:A35 4.7 79.7 1.0 P A:C37 4.8 92.0 1.0 C2' A:A35 4.9 99.2 1.0

Sodium binding site 5 out of 5 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 Sodium with other atoms in the Na 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:Na111 b:0.1 occ:1.00 OP2 A:G28 2.7 81.0 1.0 OP2 A:C27 3.6 89.3 1.0 P A:G28 4.1 85.7 1.0 O5' A:C27 4.1 74.3 1.0 N7 A:G28 4.2 87.2 1.0 P A:C27 4.3 85.2 1.0 C8 A:G28 4.5 86.8 1.0 O5' A:G28 4.6 80.9 1.0 OP1 A:C27 4.7 94.0 1.0 C3' A:C27 4.8 81.2 1.0 O3' A:C27 4.9 83.7 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