Magnesium in PDB 4oqu: Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92))

The structure of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92)), PDB code: 4oqu was solved by J.J.Trausch, F.E.Reyes, A.L.Edwards, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.41 / 3.20
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	127.269, 127.269, 181.609, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.6

The binding sites of Magnesium atom in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92)) (pdb code 4oqu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92)), PDB code: 4oqu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92))


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:68.9 occ:1.00 N7 A:G46 4.0 87.1 1.0 O6 A:G46 4.1 91.4 1.0 N1 A:A26 4.2 98.4 1.0 N7 A:G45 4.2 0.7 1.0 O6 A:G45 4.2 0.7 1.0 N1 A:A25 4.3 97.0 1.0 C2 A:A26 4.4 0.1 1.0 O2' A:A43 4.4 98.5 1.0 C5 A:G45 4.8 83.9 1.0 C6 A:G45 4.8 89.7 1.0 C5 A:G46 4.8 88.9 1.0 N6 A:A25 4.8 99.5 1.0 C6 A:G46 4.8 90.1 1.0

Magnesium binding site 2 out of 5 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92))


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:0.3 occ:1.00 OP2 A:A26 3.9 91.8 1.0 N7 A:A26 4.1 0.7 1.0 OP2 A:A25 4.4 89.0 1.0 C8 A:A26 4.6 0.4 1.0 O5' A:A25 4.6 0.2 1.0 P A:A25 4.9 0.4 1.0

Magnesium binding site 3 out of 5 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92))


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:92.6 occ:1.00 O6 A:G83 3.8 0.5 1.0 N7 A:G82 3.9 0.5 1.0 O6 A:G82 4.0 0.5 1.0 N7 A:G83 4.2 0.3 1.0 C5 A:G82 4.5 0.8 1.0 C6 A:G82 4.5 0.8 1.0 C6 A:G83 4.6 0.1 1.0 C5 A:G83 4.8 0.0 1.0 C8 A:G82 4.8 0.9 1.0

Magnesium binding site 4 out of 5 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92))


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:0.2 occ:1.00 O6 A:G58 3.7 0.5 1.0 OP2 A:G60 3.7 98.2 1.0 N7 A:G58 3.7 0.5 1.0 OP1 A:G60 4.0 0.2 1.0 C6 A:G58 4.0 0.4 1.0 C5 A:G58 4.0 0.2 1.0 P A:G60 4.3 0.7 1.0 C8 A:G58 4.6 0.3 1.0 O3' A:A59 4.7 0.4 1.0 C5' A:A59 4.9 0.4 1.0 N1 A:G58 5.0 0.0 1.0 C4 A:G58 5.0 1.0 1.0

Magnesium binding site 5 out of 5 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92))


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:99.2 occ:1.00 OP2 A:A33 2.9 0.3 1.0 O6 A:G36 3.7 0.1 1.0 P A:A33 4.0 0.7 1.0 O6 A:G35 4.0 0.3 1.0 OP1 A:A33 4.0 0.8 1.0 O4 A:U93 4.4 0.2 1.0 N4 A:C94 4.7 0.5 1.0 N6 A:A37 4.9 0.2 1.0 C6 A:G36 4.9 0.7 1.0 C6 A:G35 5.0 0.1 1.0

J.J.Trausch, Z.Xu, A.L.Edwards, F.E.Reyes, P.E.Ross, R.Knight, R.T.Batey. Structural Basis For Diversity in the Sam Clan of Riboswitches. Proc.Natl.Acad.Sci.Usa V. 111 6624 2014.
ISSN: ISSN 0027-8424
PubMed: 24753586
DOI: 10.1073/PNAS.1312918111