Magnesium in PDB 6tff: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), PDB code: 6tff 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)	55.42 / 2.52
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.880, 59.844, 192.026, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 22.5

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

Bromine	(Br)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+) (pdb code 6tff). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+), PDB code: 6tff:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)


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 Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:77.7 occ:1.00 O A:HOH205 1.9 80.7 1.0 OP2 A:C9 2.0 94.2 1.0 N7 A:A10 2.0 72.1 1.0 O A:HOH203 2.1 75.2 1.0 OP2 A:A8 2.1 93.4 1.0 O A:HOH208 2.3 90.7 1.0 C8 A:A10 2.9 58.0 1.0 C5 A:A10 3.1 50.7 1.0 P A:C9 3.4 68.7 1.0 P A:A8 3.5 74.0 1.0 N6 A:A10 3.5 62.4 1.0 C6 A:A10 3.7 69.2 1.0 OP1 A:C9 4.1 65.0 1.0 N9 A:A10 4.1 52.9 1.0 OP1 A:A8 4.1 88.6 1.0 C4 A:A10 4.2 55.2 1.0 OP2 A:C14 4.3 62.6 1.0 O5' A:C9 4.3 54.9 1.0 O5' A:A8 4.3 74.3 1.0 O3' A:A8 4.3 75.0 1.0 O A:HOH201 4.4 96.8 1.0 C5' A:A8 4.4 63.6 1.0 OP2 A:C15 4.5 59.9 1.0 O3' A:A7 4.5 71.2 1.0 C5 A:C9 4.6 71.8 1.0 C3' A:A8 4.6 70.2 1.0 C6 A:C9 4.9 64.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)


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 Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:88.6 occ:1.00 O A:HOH201 1.8 96.8 1.0 OP1 A:A8 1.9 88.6 1.0 O A:HOH206 2.0 77.6 1.0 O2A A:NAD109 2.0 0.0 1.0 O A:HOH204 2.3 74.5 1.0 O2N A:NAD109 2.4 0.9 1.0 P A:A8 3.3 74.0 1.0 PA A:NAD109 3.4 0.5 1.0 PN A:NAD109 3.6 0.3 1.0 O A:HOH203 3.9 75.2 1.0 O5' A:A8 3.9 74.3 1.0 O3 A:NAD109 3.9 0.8 1.0 C5' A:A8 4.0 63.6 1.0 C5' A:A7 4.1 56.6 1.0 O1A A:NAD109 4.2 0.8 1.0 OP2 A:A8 4.2 93.4 1.0 OP2 A:C15 4.2 59.9 1.0 C3' A:A7 4.3 56.5 1.0 O5B A:NAD109 4.3 0.9 1.0 C4' A:A7 4.3 58.0 1.0 O3' A:A7 4.3 71.2 1.0 O1N A:NAD109 4.3 0.3 1.0 OP1 A:A7 4.4 80.2 1.0 OP1 A:C15 4.5 56.1 1.0 OP1 A:C14 4.5 56.4 1.0 O5D A:NAD109 4.8 0.0 1.0 P A:C15 4.9 62.5 1.0 C5D A:NAD109 4.9 0.3 1.0 O5' A:A7 4.9 59.4 1.0 O A:HOH208 5.0 90.7 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)


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 Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:72.8 occ:1.00 OP1 A:U17 1.9 81.7 1.0 O A:HOH209 2.2 79.9 1.0 P A:U17 3.4 63.8 1.0 O3' A:G16 4.0 63.0 1.0 C5' A:U17 4.3 51.4 1.0 O5' A:U17 4.3 66.4 1.0 OP2 A:U17 4.4 71.3 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)


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 Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:81.1 occ:1.00 N7 A:G38 3.8 58.9 1.0 O2' A:G36 4.1 69.1 1.0 O6 A:G38 4.4 54.1 1.0 C5 A:G38 4.6 48.0 1.0 C8 A:G38 4.6 53.4 1.0 C6 A:G38 4.8 51.3 1.0 C2' A:G36 5.0 59.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide (Nad+)


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 Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:90.2 occ:1.00 O6 A:G47 2.3 95.7 1.0 C6 A:G47 3.2 73.5 1.0 N7 A:G47 3.7 76.1 1.0 C5 A:G47 3.7 69.1 1.0 O6 A:G48 3.8 75.0 1.0 N7 A:G48 4.2 72.1 1.0 O4 A:U46 4.3 74.8 1.0 N4 A:C6 4.3 66.0 1.0 N1 A:G47 4.4 62.1 1.0 C6 A:G48 4.6 81.4 1.0 O4 A:U5 4.7 90.5 1.0 C5 A:G48 4.8 80.6 1.0 C4 A:U46 4.9 66.4 1.0 C8 A:G47 4.9 72.0 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