Sodium 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:

Magnesium

(Mg)

4 atoms

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

Sodium 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 Sodium with other atoms in the Na 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:Na105 b:89.0 occ:1.00 N3 A:C15 2.6 57.8 1.0 O2 A:C15 2.8 61.7 1.0 C2 A:C15 3.1 63.6 1.0 O6 A:G36 3.4 75.5 1.0 C6 A:G36 3.7 67.0 1.0 C4 A:C15 3.8 60.2 1.0 C5 A:G36 4.0 58.6 1.0 N4 A:C15 4.2 69.5 1.0 N7 A:G36 4.3 63.6 1.0 N1 A:G36 4.3 59.4 1.0 N1 A:C15 4.5 63.3 1.0 N4 A:C14 4.5 62.7 1.0 C4 A:G36 4.9 59.4 1.0 N3 A:A10 4.9 60.1 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na106 b:89.8 occ:1.00 O6 A:G20 3.1 84.2 1.0 O6 A:G19 3.2 86.4 1.0 O4 A:U41 3.8 77.6 1.0 N7 A:G20 4.1 85.1 1.0 C6 A:G19 4.1 83.9 1.0 C6 A:G20 4.1 79.3 1.0 N4 A:C42 4.3 77.9 1.0 C5 A:G20 4.5 79.5 1.0 N7 A:G19 4.7 82.7 1.0 C5 A:G19 4.7 83.6 1.0 C4 A:U41 4.8 73.9 1.0 O4 A:U21 4.8 86.6 1.0 N6 A:A40 5.0 81.4 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na107 b:91.9 occ:1.00 O6 A:G47 2.3 91.5 1.0 C6 A:G47 3.3 77.5 1.0 O6 A:G48 3.7 81.1 1.0 N7 A:G47 3.9 88.5 1.0 C5 A:G47 3.9 81.5 1.0 N7 A:G48 4.1 79.6 1.0 N4 A:C6 4.2 75.4 1.0 N1 A:G47 4.4 76.1 1.0 O4 A:U46 4.4 83.5 1.0 C6 A:G48 4.6 86.6 1.0 O4 A:U5 4.7 95.0 1.0 C5 A:G48 4.8 79.5 1.0 C4 A:U46 4.9 81.1 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na108 b:88.0 occ:1.00 OP2 A:A7 2.5 71.8 1.0 P A:A7 3.6 78.3 1.0 OP1 A:C15 3.7 77.0 1.0 O5' A:A7 3.9 81.3 1.0 OP1 A:G16 4.1 73.3 1.0 OP2 A:G16 4.2 62.6 1.0 OP1 A:A7 4.3 86.1 1.0 C5' A:C15 4.4 60.0 1.0 P A:G16 4.6 74.9 1.0 C2' A:A7 4.8 66.7 1.0 C8 A:A7 4.9 70.2 1.0 O3' A:C6 5.0 93.2 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