Magnesium in PDB 3tzr: Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site

The structure of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site, PDB code: 3tzr was solved by S.M.Dibrov, K.Ding, N.Brunn, M.A.Parker, B.M.Bergdahl, D.L.Wyles, T.Hermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.79 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.054, 33.582, 81.046, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.8

The binding sites of Magnesium atom in the Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site (pdb code 3tzr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site, PDB code: 3tzr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:32.6 occ:1.00 OP1 A:U56 2.6 24.1 1.0 O A:HOH80 2.8 28.1 1.0 O4 A:U59 2.8 21.9 1.0 C2' A:C55 3.4 25.7 1.0 C5 A:U56 3.5 25.9 1.0 N4 A:C58 3.5 20.7 1.0 O2' A:C55 3.6 23.3 1.0 C4 A:U59 3.7 22.0 1.0 C5 A:C58 3.7 23.5 1.0 C2 A:A53 3.8 27.0 1.0 C6 A:U56 3.8 26.6 1.0 C4 A:C58 3.9 23.6 1.0 P A:U56 4.0 23.1 1.0 C5 A:U59 4.1 22.7 1.0 O2 A:C55 4.1 27.0 1.0 N3 A:A53 4.2 26.4 1.0 C3' A:C55 4.3 25.6 1.0 O6 A:G60 4.3 21.7 1.0 O3' A:C55 4.4 28.8 1.0 C1' A:C55 4.5 28.4 1.0 C2 A:C55 4.5 29.1 1.0 O5' A:U56 4.7 22.5 1.0 N6 B:A109 4.7 24.0 1.0 C4 A:U56 4.7 28.4 1.0 N1 A:C55 4.7 30.3 1.0 C6 A:C58 4.7 21.1 1.0 N1 A:A53 4.8 26.2 1.0 N3 A:C58 4.9 23.2 1.0 N3 A:U59 5.0 25.1 1.0

Magnesium binding site 2 out of 6 in the Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg68 b:30.0 occ:1.00 OP2 A:U56 2.6 23.1 1.0 N7 A:A57 2.8 21.9 1.0 N6 A:A57 2.9 21.3 1.0 N2 A:G52 3.1 22.0 1.0 MG A:MG69 3.1 37.9 1.0 O A:HOH87 3.2 33.4 1.0 C5' A:U56 3.3 23.8 1.0 C5 A:A57 3.5 23.5 1.0 C6 A:A57 3.6 24.7 1.0 P A:U56 3.7 23.1 1.0 C03 A:SS075 3.9 24.4 1.0 O5' A:U56 4.0 22.5 1.0 C2 A:G52 4.0 24.4 1.0 C8 A:A57 4.0 24.3 1.0 C02 A:SS075 4.0 24.2 1.0 N3 A:G52 4.1 24.1 1.0 OP1 A:U56 4.3 24.1 1.0 N4 A:C58 4.5 20.7 1.0 O B:HOH69 4.6 29.3 1.0 C4' A:U56 4.7 24.5 1.0 C5 A:C58 4.7 23.5 1.0 O2 B:C112 4.7 23.8 1.0 C4 A:C58 4.7 23.6 1.0 C4 A:A57 4.8 22.9 1.0 C1' B:C112 4.8 22.6 1.0 O2 B:C111 4.9 22.6 1.0 N1 A:A57 4.9 23.9 1.0 C04 A:SS075 5.0 23.2 1.0

Magnesium binding site 3 out of 6 in the Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg69 b:37.9 occ:1.00 N3 A:G52 2.9 24.1 1.0 O4 A:SO473 3.0 59.6 1.0 O2 B:C112 3.0 23.8 1.0 O A:HOH87 3.1 33.4 1.0 O B:HOH69 3.1 29.3 1.0 MG A:MG68 3.1 30.0 1.0 N2 A:G52 3.5 22.0 1.0 C2 A:G52 3.6 24.4 1.0 O2' A:G52 3.6 31.5 1.0 S A:SO473 3.7 55.0 1.0 O3 A:SO473 3.7 43.6 1.0 N2 A:G51 3.7 23.3 1.0 C1' A:G52 3.8 27.0 1.0 O2 A:SO473 3.9 38.9 1.0 C4 A:G52 3.9 24.8 1.0 C2' A:G52 4.0 25.9 1.0 C2 B:C112 4.2 24.1 1.0 N9 A:G52 4.3 25.9 1.0 N7 A:A57 4.5 21.9 1.0 O A:HOH20 4.6 26.7 1.0 C1' B:C112 4.6 22.6 1.0 O2' B:C112 4.6 21.8 1.0 C2 A:G51 4.7 23.0 1.0 N1 B:C112 4.9 26.5 1.0 N1 A:G52 4.9 21.8 1.0 O4' A:G52 5.0 25.1 1.0 C2' B:C112 5.0 23.9 1.0 OP2 A:U56 5.0 23.1 1.0 N3 B:C112 5.0 23.8 1.0

Magnesium binding site 4 out of 6 in the Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg70 b:38.8 occ:1.00 OP2 B:C108 2.8 32.8 1.0 N7 A:A53 2.9 27.4 1.0 C A:SS075 3.1 21.4 1.0 C11 A:SS075 3.2 24.7 1.0 C15 A:SS075 3.6 24.2 1.0 C08 A:SS075 3.7 23.6 1.0 C8 A:A53 3.7 27.0 1.0 C09 A:SS075 3.9 26.2 1.0 P B:C108 4.0 32.2 1.0 N A:SS075 4.1 24.9 1.0 OP1 B:G107 4.1 60.7 1.0 C5 A:A53 4.1 26.4 1.0 C16 A:SS075 4.3 20.6 1.0 C06 A:SS075 4.3 23.4 1.0 N6 A:A53 4.3 23.7 1.0 O B:HOH71 4.4 40.7 1.0 C10 A:SS075 4.4 28.3 1.0 N04 A:SS075 4.4 37.0 1.0 OP1 B:C108 4.5 30.5 1.0 C12 A:SS075 4.5 21.6 1.0 O5' B:C108 4.6 33.8 1.0 C13 A:SS075 4.7 35.9 1.0 C6 A:A53 4.7 23.8 1.0 C05 A:SS075 4.7 21.3 1.0 O A:HOH46 4.7 25.6 1.0 N02 A:SS075 4.8 22.3 1.0 OP2 B:A109 4.9 25.7 1.0

Magnesium binding site 5 out of 6 in the Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg71 b:38.9 occ:1.00 O A:HOH83 2.6 32.9 1.0 O3' A:A54 3.4 28.8 1.0 O5' A:C55 3.8 25.3 1.0 C4' A:A54 3.9 32.5 1.0 OP2 A:C55 4.1 24.8 1.0 P A:C55 4.1 23.9 1.0 C5' A:C55 4.1 24.6 1.0 O4' A:A54 4.1 29.6 1.0 C3' A:A54 4.3 28.4 1.0 OP2 A:A54 4.4 26.7 1.0 O4' A:C55 4.4 25.7 1.0 C6 A:C55 4.5 26.9 1.0 C1' A:A54 4.8 28.1 1.0 C5 A:C55 4.9 27.6 1.0 C4' A:C55 4.9 28.2 1.0

Magnesium binding site 6 out of 6 in the Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Riboswitch-Like Rna-Ligand Complex From the Hepatitis C Virus Internal Ribosome Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:28.9 occ:1.00 O A:HOH8 2.8 24.4 1.0 O2' B:C114 2.9 21.9 1.0 O4' B:G115 3.1 22.4 1.0 O2 B:C114 3.7 22.9 1.0 C2' B:C114 3.8 23.6 1.0 C1' B:G115 4.0 23.6 1.0 C4' B:G115 4.0 25.0 1.0 C1' B:C114 4.3 24.8 1.0 C5' B:G115 4.3 23.0 1.0 N2 A:G49 4.4 19.3 1.0 N9 B:G115 4.7 27.8 1.0 C2 B:C114 4.7 25.1 1.0

T.Hermann, S.Dibrov, K.Ding, N.Brunn, M.Parker, M.Bergdahl, D.Wyles. Structure of A Riboswitch in the Hepatitis C Virus Internal Ribosome Entry Site To Be Published.