Magnesium in PDB 4qk8: Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch

The structure of Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch, PDB code: 4qk8 was solved by A.Gao, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.72 / 3.05
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.868, 114.868, 114.709, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 19.5

The structure of Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch (pdb code 4qk8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch, PDB code: 4qk8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:64.5 occ:1.00 OP2 A:G27 2.0 66.5 1.0 OP2 A:C95 2.1 70.7 1.0 O4 A:U96 2.3 65.7 1.0 OP1 A:G94 2.6 71.4 1.0 C4 A:U96 3.3 71.0 1.0 P A:C95 3.4 72.6 1.0 O3' A:A93 3.5 66.7 1.0 P A:G27 3.5 63.1 1.0 OP1 A:G26 3.6 64.8 1.0 P A:G94 3.6 71.2 1.0 C5 A:U96 3.9 72.6 1.0 O5' A:G26 3.9 63.8 1.0 OP1 A:C95 4.0 69.0 1.0 P A:G26 4.1 63.7 1.0 N7 A:G27 4.2 66.5 1.0 O2' A:A93 4.2 65.9 1.0 O3' A:G26 4.2 60.5 1.0 C3' A:G26 4.3 61.5 1.0 O5' A:G27 4.3 63.5 1.0 OP2 A:G26 4.3 68.5 1.0 C5' A:G94 4.3 69.3 1.0 O3' A:G94 4.3 71.2 1.0 C5' A:G26 4.3 64.4 1.0 O5' A:G94 4.4 68.7 1.0 OP1 A:G27 4.5 62.9 1.0 C8 A:G27 4.5 65.0 1.0 O5' A:C95 4.5 70.6 1.0 N3 A:U96 4.6 68.6 1.0 C3' A:G94 4.6 72.5 1.0 C3' A:A93 4.8 66.8 1.0 OP2 A:G94 4.9 67.5 1.0 C4' A:G26 4.9 62.3 1.0 C2' A:A93 5.0 65.6 1.0

Magnesium binding site 2 out of 4 in the Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:78.0 occ:1.00 OP1 A:U43 2.5 65.4 1.0 OP1 A:A25 2.6 64.1 1.0 P A:U43 3.9 64.5 1.0 P A:A25 4.0 59.7 1.0 O3' A:G24 4.6 61.6 1.0 OP2 A:U44 4.7 60.7 1.0 O5' A:U43 4.7 62.1 1.0 OP2 A:U43 4.7 61.7 1.0 OP2 A:A25 4.8 60.3 1.0 O3' A:G42 4.9 62.8 1.0

Magnesium binding site 3 out of 4 in the Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:56.8 occ:1.00 OP2 A:G94 2.1 67.5 1.0 P A:G94 3.4 71.2 1.0 OP1 A:G94 3.9 71.4 1.0 OP1 A:A28 4.0 71.4 1.0 OP1 A:G27 4.1 62.9 1.0 O3' A:A93 4.3 66.7 1.0 OP2 A:A28 4.3 68.9 1.0 C4' A:A93 4.5 65.8 1.0 N4 A:C95 4.5 75.5 1.0 O5' A:G94 4.5 68.7 1.0 N7 A:G94 4.5 77.1 1.0 P A:A28 4.7 68.2 1.0 C5' A:A93 4.8 67.4 1.0 C8 A:G94 4.8 74.5 1.0 C3' A:A93 4.9 66.8 1.0 P A:G27 5.0 63.1 1.0

Magnesium binding site 4 out of 4 in the Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermoanaerobacter Pseudethanolicus C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:71.3 occ:1.00 OP1 A:C7 2.6 60.4 1.0 OP1 A:A70 2.7 59.9 1.0 P A:A70 3.9 60.1 1.0 P A:C7 4.0 56.5 1.0 O3' A:G69 4.1 63.0 1.0 OP2 A:G8 4.2 56.3 1.0 OP2 A:A70 4.6 59.9 1.0 O5' A:C7 4.6 57.4 1.0 OP2 A:C7 4.7 57.5 1.0 C5' A:C7 4.8 58.1 1.0

A.Gao, A.Serganov. Structural Insights Into Recognition of C-Di-Amp By the Ydao Riboswitch. Nat.Chem.Biol. V. 10 787 2014.
ISSN: ISSN 1552-4450
PubMed: 25086507
DOI: 10.1038/NCHEMBIO.1607