Magnesium in PDB 4l81: Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))

The structure of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)), PDB code: 4l81 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)	30.00 / 2.95
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.930, 120.930, 186.560, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 23.2

The structure of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) also contains other interesting chemical elements:

Cobalt

(Co)

9 atoms

The binding sites of Magnesium atom in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) (pdb code 4l81). 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 the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)), PDB code: 4l81:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


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, DELTAG93)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:79.3 occ:1.00 N7 A:G91 2.9 73.7 1.0 O6 A:G91 3.0 71.5 1.0 C5 A:G91 3.5 71.8 1.0 C6 A:G91 3.6 71.3 1.0 C8 A:G91 4.0 74.4 1.0 N6 A:A90 4.0 66.7 1.0 C6 A:A90 4.5 62.7 1.0 C4 A:G91 4.8 72.6 1.0 N1 A:A90 4.8 61.3 1.0 N1 A:G91 4.9 71.2 1.0

Magnesium binding site 2 out of 6 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


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, DELTAG93)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg112 b:81.4 occ:1.00 N7 A:G31 2.4 56.8 1.0 O6 A:G31 2.8 64.1 1.0 C5 A:G31 3.1 58.6 1.0 C6 A:G31 3.3 61.6 1.0 N7 A:G30 3.3 56.5 1.0 N2 A:NCO107 3.4 0.7 1.0 C8 A:G31 3.5 58.8 1.0 N5 A:NCO107 3.6 0.7 1.0 C5 A:G30 3.8 56.8 1.0 C8 A:G30 4.0 57.5 1.0 C6 A:G30 4.1 57.6 1.0 O6 A:G30 4.1 58.9 1.0 N7 A:G32 4.3 68.4 1.0 C4 A:G31 4.4 59.4 1.0 O6 A:G32 4.5 69.6 1.0 N3 A:NCO107 4.5 0.6 1.0 CO A:NCO107 4.5 0.0 1.0 C4 A:G30 4.6 58.9 1.0 N9 A:G31 4.6 60.9 1.0 N1 A:G31 4.6 61.2 1.0 N9 A:G30 4.7 59.6 1.0 C5 A:G32 4.9 68.4 1.0 C6 A:G32 5.0 69.1 1.0

Magnesium binding site 3 out of 6 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


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, DELTAG93)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg113 b:81.2 occ:1.00 O2' A:G30 2.4 61.4 1.0 N3 A:G30 2.5 61.2 1.0 C2' A:G30 2.7 62.9 1.0 C1' A:G30 2.7 61.2 1.0 OP2 A:C87 3.0 76.2 1.0 C4 A:G30 3.3 58.9 1.0 N9 A:G30 3.4 59.6 1.0 C2 A:G30 3.5 62.1 1.0 C2 A:A44 3.6 59.9 1.0 N3 A:A44 3.8 59.3 1.0 O4' A:G31 3.8 67.6 1.0 N2 A:G30 3.8 64.8 1.0 C2' A:A86 3.8 73.8 1.0 O4' A:G30 4.0 64.5 1.0 O2' A:A86 4.1 71.9 1.0 C3' A:G30 4.2 65.7 1.0 P A:C87 4.3 79.3 1.0 N1 A:A44 4.3 56.8 1.0 C3' A:A86 4.5 76.0 1.0 C1' A:G31 4.5 64.8 1.0 O3' A:A86 4.5 77.9 1.0 C4 A:A44 4.6 60.8 1.0 C4' A:G30 4.6 64.0 1.0 C5 A:G30 4.6 56.8 1.0 C8 A:G30 4.7 57.5 1.0 N9 A:G31 4.8 60.9 1.0 C8 A:G31 4.8 58.8 1.0 N1 A:G30 4.8 58.5 1.0 C4' A:G31 4.9 66.2 1.0 C1' A:A86 5.0 73.5 1.0 N9 A:A86 5.0 72.7 1.0 O3' A:G30 5.0 68.7 1.0 OP1 A:C87 5.0 78.9 1.0

Magnesium binding site 4 out of 6 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


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, DELTAG93)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg114 b:94.4 occ:1.00 OP3 A:G1 2.5 80.3 1.0 P A:G1 3.9 84.0 1.0 OP2 A:G1 4.4 76.4 1.0 C5' A:G1 4.6 72.8 1.0 O5' A:G1 4.8 77.1 1.0 OP1 A:G1 4.9 82.5 1.0

Magnesium binding site 5 out of 6 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


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, DELTAG93)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg115 b:99.9 occ:1.00 O2' A:G58 2.6 98.6 1.0 N7 A:A59 2.8 88.9 1.0 C8 A:A59 3.5 89.3 1.0 O6 A:G60 3.5 86.3 1.0 O3' A:G58 3.5 0.7 1.0 C2' A:G58 3.9 99.9 1.0 OP1 A:A59 4.0 97.8 1.0 C5 A:A59 4.0 88.1 1.0 C3' A:G58 4.2 0.6 1.0 C6 A:G60 4.3 84.8 1.0 N6 A:A59 4.4 87.5 1.0 P A:A59 4.4 0.0 1.0 N7 A:G60 4.5 84.8 1.0 C4' A:G58 4.6 0.5 1.0 C5 A:G60 4.7 84.5 1.0 C6 A:A59 4.7 88.0 1.0 N9 A:A59 4.8 89.3 1.0 C1' A:G58 4.9 99.5 1.0

Magnesium binding site 6 out of 6 in the Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93))


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Sam-I/IV Riboswitch (ENV87(DELTAU92, DELTAG93)) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg116 b:0.7 occ:1.00 O6 A:G73 2.8 70.9 1.0 O6 A:G72 3.2 74.0 1.0 N7 A:G73 3.4 73.1 1.0 N7 A:G72 3.6 70.1 1.0 C6 A:G73 3.6 72.7 1.0 C6 A:G72 3.7 69.6 1.0 C5 A:G73 3.9 72.8 1.0 C5 A:G72 3.9 69.4 1.0 C8 A:G73 4.6 72.9 1.0 C8 A:G72 4.7 71.3 1.0 N4 A:C84 4.8 79.0 1.0 N6 A:A85 4.8 79.2 1.0 N6 A:NCO106 4.8 0.0 1.0 N1 A:G72 4.9 67.5 1.0 N4 A:C74 4.9 74.8 1.0 N1 A:G73 5.0 72.7 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