Sodium in PDB 6tf0: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh), PDB code: 6tf0 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)	32.11 / 2.10
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.272, 59.230, 191.085, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.8

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh) also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Bromine	(Br)	1 atom

The binding sites of Sodium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh) (pdb code 6tf0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh), PDB code: 6tf0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:74.2 occ:1.00 O6 A:G36 2.5 78.1 1.0 O2 A:C15 2.5 53.8 1.0 N3 A:C15 2.6 55.8 1.0 C2 A:C15 2.9 58.4 1.0 C6 A:G36 3.0 70.2 1.0 C5 A:G36 3.7 67.4 1.0 N1 A:G36 3.8 67.0 1.0 C4 A:C15 3.8 64.0 1.0 N4 A:C14 3.9 64.2 1.0 N7 A:G36 4.0 70.2 1.0 N4 A:C15 4.2 63.2 1.0 N1 A:C15 4.3 62.0 1.0 O A:HOH204 4.5 58.4 1.0 C4 A:C14 4.7 67.6 1.0 C4 A:G36 4.7 65.6 1.0 N3 A:C14 4.7 65.1 1.0 C2 A:G36 4.8 64.8 1.0 N3 A:A10 4.9 57.4 1.0 C5 A:C15 5.0 61.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh)


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 Nicotinamide Adenine Dinucleotide, Reduced (Nadh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na110 b:98.4 occ:1.00 O6 A:G28 3.9 87.1 1.0 N7 A:G28 4.0 74.9 1.0 C6 A:G28 4.4 82.2 1.0 C5 A:G28 4.5 79.1 1.0 OP1 A:A30 4.5 95.3 1.0 OP2 A:A30 4.9 80.6 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