Magnesium in PDB 4w92: Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao

The structure of Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao, PDB code: 4w92 was solved by C.P.Jones, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.79 / 3.21
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.281, 83.062, 233.573, 90.00, 90.00, 90.00
R / Rfree (%)	25.2 / 28.9

The structure of Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao (pdb code 4w92). 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 Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao, PDB code: 4w92:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao


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 Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:42.6 occ:1.00 OP1 C:U62 2.1 82.5 1.0 OP1 C:G27 2.3 84.7 1.0 P C:U62 3.6 82.6 1.0 P C:G27 3.6 86.1 1.0 O3' C:G26 4.1 85.8 1.0 O3' C:G61 4.3 84.0 1.0 OP2 C:G27 4.3 86.8 1.0 OP2 C:U62 4.4 81.8 1.0 OP2 C:G63 4.4 81.1 1.0 O5' C:U62 4.5 82.8 1.0 C5' C:U62 4.7 83.9 1.0 O5' C:G27 4.8 0.5 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao


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 Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:60.5 occ:1.00 OP2 C:C102 2.0 0.7 1.0 O4 C:U103 2.1 0.6 1.0 OP1 C:G101 2.2 0.1 1.0 OP2 C:G29 2.5 0.8 1.0 C4 C:U103 3.1 0.2 1.0 P C:C102 3.5 97.7 1.0 P C:G101 3.6 0.3 1.0 N7 C:G29 3.6 94.7 1.0 C5 C:U103 3.6 0.4 1.0 P C:G29 3.9 96.2 1.0 C8 C:G29 3.9 96.3 1.0 O3' C:A100 4.0 0.1 1.0 O5' C:G29 4.2 97.6 1.0 OP1 C:C102 4.2 95.8 1.0 N3 C:U103 4.3 0.7 1.0 O5' C:C102 4.4 97.4 1.0 O3' C:G101 4.4 97.1 1.0 O5' C:G28 4.4 0.3 1.0 OP2 C:G101 4.5 0.4 1.0 O5' C:G101 4.5 0.1 1.0 OP1 C:G28 4.5 95.3 1.0 C3' C:G101 4.6 98.8 1.0 C3' C:G28 4.8 96.3 1.0 C5' C:G101 4.8 0.9 1.0 C5' C:G28 4.8 0.2 1.0 OP2 C:G28 4.8 89.3 1.0 P C:G28 4.8 89.8 1.0 O3' C:G28 4.8 96.7 1.0 C5 C:G29 4.8 95.5 1.0 OP1 C:G29 4.9 0.7 1.0 C5 C:C102 4.9 0.2 1.0 C6 C:U103 5.0 0.4 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao


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 Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:55.8 occ:1.00 OP2 C:A20 3.4 0.1 1.0 OP1 C:C19 4.4 0.7 1.0 N7 C:A20 4.6 0.5 1.0 P C:A20 4.7 0.0 1.0 C8 C:A20 4.9 0.6 1.0 O5' C:A20 5.0 0.6 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao


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 Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg204 b:44.6 occ:1.00 OP1 C:U7 2.0 80.2 1.0 OP1 C:C82 2.4 95.7 1.0 P C:U7 3.4 80.7 1.0 P C:C82 3.8 68.4 1.0 OP2 C:U7 4.1 82.1 1.0 O3' C:G81 4.2 71.5 1.0 OP2 C:U8 4.3 79.4 1.0 O5' C:U7 4.3 80.0 1.0 O3' C:C6 4.4 80.6 1.0 O5' C:C82 4.7 68.0 1.0 C5' C:U7 4.7 97.9 1.0 OP2 C:C82 4.8 68.0 1.0 C5' C:C82 4.9 68.9 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao


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 Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg205 b:33.3 occ:1.00 OP2 C:G101 2.5 0.4 1.0 OP1 C:G29 3.9 0.7 1.0 P C:G101 4.0 0.3 1.0 OP2 C:A30 4.0 98.9 1.0 C4' C:A100 4.7 0.2 1.0 C5' C:A100 4.7 0.2 1.0 OP1 C:G101 4.7 0.1 1.0 O3' C:A100 4.8 0.1 1.0 O5' C:G101 4.9 0.1 1.0 P C:G29 4.9 96.2 1.0

C.P.Jones, A.R.Ferre-D'amare. Crystal Structure of A C-Di-Amp Riboswitch Reveals An Internally Pseudo-Dimeric Rna. Embo J. 2014.
ISSN: ESSN 1460-2075
PubMed: 25271255
DOI: 10.15252/EMBJ.201489209