Sodium in PDB 6tfe: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP), PDB code: 6tfe 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)	47.52 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.350, 59.440, 190.070, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 25.7

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) also contains other interesting chemical elements:

Magnesium	(Mg)	10 atoms
Bromine	(Br)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) (pdb code 6tfe). 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 N6-Methyl-Adenosine-5'-Triphosphate (M6ATP), PDB code: 6tfe:
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 N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na113 b:68.9 occ:1.00 N3 A:C15 2.7 54.1 1.0 O2 A:C15 2.8 49.5 1.0 O6 A:G36 3.1 74.2 1.0 C2 A:C15 3.1 66.6 1.0 C6 A:G36 3.5 90.9 1.0 H42 A:C14 3.6 92.3 1.0 H42 A:C15 3.8 79.3 1.0 C4 A:C15 3.9 57.0 1.0 C5 A:G36 3.9 62.9 1.0 N4 A:C14 4.2 76.4 1.0 N7 A:G36 4.2 74.9 1.0 N1 A:G36 4.2 72.9 1.0 N4 A:C15 4.2 65.6 1.0 H1 A:G36 4.3 88.0 1.0 H41 A:C14 4.5 92.3 1.0 N1 A:C15 4.5 50.2 1.0 H2 A:A10 4.8 84.7 1.0 N3 A:A10 4.8 62.4 1.0 H1' A:A10 4.8 0.3 1.0 C4 A:G36 4.9 99.5 1.0 C4 A:C14 4.9 61.9 1.0 N3 A:C14 5.0 62.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na114 b:0.1 occ:1.00 O6 A:G20 2.9 83.4 1.0 O6 A:G19 3.2 66.1 1.0 N7 A:G20 3.6 0.3 1.0 C6 A:G20 3.8 80.4 1.0 O4 A:U41 3.9 80.4 1.0 H42 A:C42 4.0 87.8 1.0 C6 A:G19 4.0 82.4 1.0 C5 A:G20 4.1 0.9 1.0 H3 A:U41 4.2 82.8 1.0 MG A:MG108 4.3 0.8 1.0 H61 A:A40 4.3 92.4 1.0 N4 A:C42 4.4 72.7 1.0 H41 A:C42 4.5 87.8 1.0 O4 A:U21 4.5 67.7 1.0 H62 A:A40 4.5 92.4 1.0 C5 A:G19 4.6 0.9 1.0 N7 A:G19 4.7 69.7 1.0 N6 A:A40 4.7 76.5 1.0 C4 A:U41 4.8 68.4 1.0 N3 A:U41 4.8 68.5 1.0 C8 A:G20 4.9 0.3 1.0 N1 A:G19 4.9 55.6 1.0 H1 A:G19 4.9 67.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na115 b:97.8 occ:1.00 H5 A:C37 3.5 58.7 1.0 HO2' A:A35 3.7 0.3 1.0 N7 A:A35 3.9 94.2 1.0 OP1 A:C37 3.9 87.7 1.0 O2' A:A35 4.0 0.3 1.0 C8 A:A35 4.0 0.3 1.0 C5 A:A35 4.0 0.6 1.0 C4 A:A35 4.3 0.6 1.0 N9 A:A35 4.3 0.9 1.0 H8 A:A35 4.3 0.7 1.0 H6 A:C37 4.3 74.5 1.0 H2' A:A35 4.4 0.9 1.0 C5 A:C37 4.4 48.4 1.0 OP2 A:C37 4.6 0.2 1.0 C6 A:A35 4.6 92.5 1.0 C2' A:A35 4.7 0.8 1.0 P A:C37 4.7 91.5 1.0 C6 A:C37 4.8 61.6 1.0 H62 A:A35 4.9 0.1 1.0 N6 A:A35 5.0 0.8 1.0 N3 A:A35 5.0 0.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with N6-Methyl-Adenosine-5'-Triphosphate (M6ATP)


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 N6-Methyl-Adenosine-5'-Triphosphate (M6ATP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na116 b:0.5 occ:1.00 O6 A:G28 3.7 87.1 1.0 N7 A:G28 3.9 69.6 1.0 OP1 A:A30 4.1 88.6 1.0 C6 A:G28 4.2 65.8 1.0 C5 A:G28 4.3 0.4 1.0 OP2 A:A30 4.6 71.6 1.0 H5'' A:A29 4.8 83.8 1.0 P A:A30 4.9 81.3 1.0 C8 A:G28 4.9 0.3 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