Magnesium in PDB 4w90: 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: 4w90 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)	46.94 / 3.12
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.280, 84.850, 230.536, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 28.8

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Subtilis Cyclic-Di-Amp Riboswitch Ydao (pdb code 4w90). 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: 4w90:
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:Mg203 b:40.1 occ:1.00 OP2 C:G101 2.3 0.4 1.0 P C:G101 3.7 0.4 1.0 OP1 C:A30 3.9 99.3 1.0 OP1 C:G29 4.1 94.6 1.0 OP1 C:G101 4.4 0.6 1.0 OP2 C:A30 4.5 92.9 1.0 O3' C:A100 4.5 0.4 1.0 C4' C:A100 4.6 93.4 1.0 O5' C:G101 4.7 89.8 1.0 P C:A30 4.7 93.7 1.0 C5' C:A100 4.8 90.8 1.0 N7 C:G101 4.9 96.5 1.0 C3' C:A100 4.9 0.1 1.0 P C:G29 5.0 94.3 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:Mg204 b:70.1 occ:1.00 OP1 C:C82 2.3 0.6 1.0 OP1 C:U7 2.3 92.6 1.0 P C:U7 3.7 73.7 1.0 P C:C82 3.7 74.9 1.0 O3' C:G81 4.3 85.6 1.0 OP2 C:U7 4.3 83.8 1.0 O3' C:C6 4.6 85.1 1.0 O5' C:C82 4.6 76.8 1.0 OP2 C:C82 4.7 72.0 1.0 O5' C:U7 4.7 60.4 1.0 OP2 C:U8 4.7 64.4 1.0 C5' C:C82 4.8 79.8 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:Mg205 b:86.7 occ:1.00 OP1 C:G27 2.1 85.4 1.0 OP1 C:U62 2.2 83.5 1.0 P C:G27 3.5 79.3 1.0 P C:U62 3.7 83.8 1.0 O3' C:G26 4.0 87.0 1.0 OP2 C:G63 4.3 80.3 1.0 OP2 C:G27 4.4 67.3 1.0 O5' C:U62 4.4 87.4 1.0 OP2 C:U62 4.6 80.1 1.0 O5' C:G27 4.6 79.6 1.0 O3' C:G61 4.7 77.1 1.0 C5' C:U62 4.7 83.4 1.0 C5' C:G27 4.9 82.7 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:Mg206 b:56.5 occ:1.00 O6 C:G79 3.0 86.4 1.0 O6 C:G80 3.0 94.1 1.0 N7 C:G79 3.5 80.0 1.0 N7 C:G80 3.5 70.6 1.0 C6 C:G79 3.6 76.9 1.0 C6 C:G80 3.7 84.1 1.0 C5 C:G79 3.8 75.5 1.0 C5 C:G80 3.9 76.5 1.0 OP2 C:A78 4.2 0.5 1.0 C8 C:G79 4.6 76.2 1.0 C8 C:G80 4.6 65.9 1.0 N1 C:G79 4.8 76.1 1.0 N4 C:C90 5.0 82.1 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:Mg207 b:68.2 occ:1.00 OP1 C:G101 2.1 0.6 1.0 OP2 C:C102 2.2 0.4 1.0 OP2 C:G29 2.3 98.9 1.0 O4 C:U103 2.6 84.1 1.0 P C:G101 3.4 0.4 1.0 P C:C102 3.5 1.0 1.0 O3' C:A100 3.5 0.4 1.0 O5' C:G28 3.7 92.0 1.0 C4 C:U103 3.7 86.0 1.0 OP1 C:G28 3.7 0.6 1.0 P C:G29 3.7 94.3 1.0 N7 C:G29 3.8 0.0 1.0 P C:G28 3.9 0.0 1.0 OP1 C:C102 4.0 0.7 1.0 OP2 C:G28 4.1 94.0 1.0 C5 C:U103 4.1 92.2 1.0 O3' C:G101 4.1 83.0 1.0 C8 C:G29 4.2 0.8 1.0 C5' C:G101 4.2 91.9 1.0 O5' C:G101 4.2 89.8 1.0 O5' C:G29 4.3 0.1 1.0 C5' C:G28 4.3 94.3 1.0 C3' C:G101 4.4 85.1 1.0 OP2 C:G101 4.5 0.4 1.0 C3' C:G28 4.5 0.4 1.0 O3' C:G28 4.6 0.8 1.0 O5' C:C102 4.6 96.1 1.0 OP1 C:G29 4.7 94.6 1.0 O2' C:A100 4.8 93.2 1.0 N3 C:U103 4.9 94.9 1.0 C4' C:G101 4.9 86.8 1.0 C3' C:A100 4.9 0.1 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