Magnesium in PDB 6vwt: Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding

The structure of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding, PDB code: 6vwt was solved by J.R.Stagno, Y.-X.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.17 / 3.03
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.340, 25.200, 78.740, 99.29, 90.55, 90.21
R / Rfree (%)	22.6 / 25

The binding sites of Magnesium atom in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding (pdb code 6vwt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding, PDB code: 6vwt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:89.4 occ:1.00 OP1 A:G13 2.1 0.0 1.0 P A:G13 3.3 0.9 1.0 OP2 A:G13 3.7 0.4 1.0 O5' A:G13 4.0 0.6 1.0 MG A:MG103 4.2 0.1 1.0 C5' A:G13 4.4 0.6 1.0 OP3 A:G13 4.4 0.9 1.0

Magnesium binding site 2 out of 8 in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:0.1 occ:1.00 OP2 A:G13 2.0 0.4 1.0 P A:G13 3.3 0.9 1.0 O5' A:G13 3.7 0.6 1.0 OP1 A:G13 4.0 0.0 1.0 MG A:MG102 4.2 89.4 1.0 OP3 A:G13 4.4 0.9 1.0

Magnesium binding site 3 out of 8 in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:68.5 occ:1.00 OP2 A:A23 2.1 73.0 1.0 P A:A23 3.5 75.0 1.0 O3' A:U22 3.9 71.2 1.0 O5' A:A23 4.3 72.7 1.0 O2' A:U22 4.3 76.4 1.0 OP1 A:A23 4.6 72.5 1.0 C5' A:A23 4.6 73.1 1.0 N6 A:ADE101 4.7 71.0 1.0 C3' A:U22 4.9 75.0 1.0 N6 A:A21 4.9 71.7 1.0 N7 A:A21 4.9 79.9 1.0

Magnesium binding site 4 out of 8 in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:77.8 occ:1.00 OP1 A:A24 2.1 66.4 1.0 P A:A24 3.5 75.2 1.0 O3' A:A23 4.0 71.2 1.0 O5' A:A24 4.2 69.7 1.0 N7 A:A24 4.5 63.3 1.0 O6 A:G72 4.5 71.7 1.0 OP2 A:A24 4.6 74.2 1.0 C5 A:U71 4.6 74.7 1.0 O4 A:U71 4.6 74.8 1.0 C8 A:A24 4.7 63.5 1.0 N7 A:G72 4.7 69.7 1.0 C4 A:U71 4.8 73.5 1.0

Magnesium binding site 5 out of 8 in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:92.2 occ:1.00 OP1 B:G13 2.1 0.2 1.0 P B:G13 3.2 0.2 1.0 OP2 B:G13 3.5 0.2 1.0 MG B:MG103 3.7 0.8 1.0 O5' B:G13 4.1 0.1 1.0 OP3 B:G13 4.3 0.1 1.0 C5' B:G13 4.6 0.7 1.0

Magnesium binding site 6 out of 8 in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:0.8 occ:1.00 OP2 B:G13 1.9 0.2 1.0 P B:G13 2.9 0.2 1.0 O5' B:G13 3.2 0.1 1.0 OP1 B:G13 3.6 0.2 1.0 MG B:MG102 3.7 92.2 1.0 OP3 B:G13 4.2 0.1 1.0 C5' B:G13 4.5 0.7 1.0

Magnesium binding site 7 out of 8 in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:62.3 occ:1.00 OP2 B:A23 2.1 72.1 1.0 P B:A23 3.5 73.6 1.0 O3' B:U22 4.0 69.6 1.0 O5' B:A23 4.3 72.8 1.0 C5' B:A23 4.5 72.8 1.0 O2' B:U22 4.5 75.2 1.0 OP1 B:A23 4.7 70.2 1.0 N6 B:ADE101 4.8 71.0 1.0

Magnesium binding site 8 out of 8 in the Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Transitional Unit Cell 1 of Adenine Riboswitch Aptamer Crystal Phase Transition Upon Ligand Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:72.1 occ:1.00 OP1 B:A24 2.0 67.6 1.0 P B:A24 3.4 75.7 1.0 O3' B:A23 4.0 70.6 1.0 O5' B:A24 4.1 70.0 1.0 O6 B:G72 4.4 71.9 1.0 N7 B:A24 4.5 64.8 1.0 OP2 B:A24 4.6 74.8 1.0 C8 B:A24 4.6 65.0 1.0 O4 B:U71 4.6 73.8 1.0 C5 B:U71 4.6 74.1 1.0 N7 B:G72 4.6 68.6 1.0 C4 B:U71 4.8 73.3 1.0

S.Ramakrishnan, J.R.Stagno, C.Conrad, J.Ding, P.Yu, Y.Bhandari, A.Cantero-Camacho, Y.-T.Lee, G.Pauly, O.Yefanov, M.Wiedorn, J.Knoska, D.Oberthuer, T.A.White, A.Barty, V.Mariani, W.F.Heinz, V.Magidson, S.Lockett, M.S.Hunter, S.Boutet, N.Zatsepin, C.Li, T.D.Grant, J.C.H.Spence, H.N.Chapman, Y.-X.Wang. Synchronized Behaviors of Riboswitch Molecules in Crystals To Be Published.