Magnesium in PDB 4qk9: Thermovirga Lienii C-Di-Amp Riboswitch

The structure of Thermovirga Lienii C-Di-Amp Riboswitch, PDB code: 4qk9 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)	29.47 / 3.05
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	110.265, 110.265, 110.265, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Thermovirga Lienii C-Di-Amp Riboswitch (pdb code 4qk9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Thermovirga Lienii C-Di-Amp Riboswitch, PDB code: 4qk9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Thermovirga Lienii 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 Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:47.4 occ:1.00 OP2 A:G30 2.0 46.6 1.0 OP2 A:C99 2.2 44.7 1.0 OP1 A:G98 2.4 46.2 1.0 O4 A:U100 2.5 46.0 1.0 O3' A:A97 3.5 52.8 1.0 P A:C99 3.5 37.6 1.0 P A:G98 3.5 52.2 1.0 P A:G30 3.5 44.2 1.0 C4 A:U100 3.5 46.8 1.0 OP1 A:G29 3.6 39.2 1.0 O5' A:G29 3.9 44.3 1.0 C5 A:U100 4.1 45.9 1.0 O3' A:G98 4.1 41.0 1.0 P A:G29 4.1 42.5 1.0 OP1 A:C99 4.2 40.8 1.0 N7 A:G30 4.2 44.2 1.0 O5' A:G30 4.3 39.5 1.0 O3' A:G29 4.3 47.7 1.0 C5' A:G98 4.4 46.0 1.0 O5' A:G98 4.4 45.0 1.0 OP2 A:G29 4.4 45.0 1.0 C5' A:G29 4.4 41.5 1.0 C3' A:G29 4.4 42.9 1.0 C3' A:G98 4.4 42.8 1.0 OP1 A:G30 4.4 48.4 1.0 C8 A:G30 4.5 44.7 1.0 O2' A:A97 4.6 52.0 1.0 O5' A:C99 4.7 44.5 1.0 OP2 A:G98 4.7 54.3 1.0 N3 A:U100 4.8 43.7 1.0 C3' A:A97 4.8 54.3 1.0 C4' A:G98 5.0 44.9 1.0

Magnesium binding site 2 out of 11 in the Thermovirga Lienii 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 Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:40.4 occ:1.00 OP1 A:U47 2.1 42.4 1.0 OP1 A:G28 2.6 44.7 1.0 P A:U47 3.6 42.9 1.0 P A:G28 3.9 38.6 1.0 O3' A:G27 4.3 42.7 1.0 OP2 A:G48 4.3 40.0 1.0 O5' A:U47 4.4 40.6 1.0 O3' A:G46 4.4 43.7 1.0 OP2 A:G28 4.5 36.8 1.0 OP2 A:U47 4.5 40.9 1.0 C5' A:U47 4.7 40.9 1.0

Magnesium binding site 3 out of 11 in the Thermovirga Lienii 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 Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:42.4 occ:1.00 N7 A:G48 4.4 45.6 1.0 OP1 A:A50 4.5 42.1 1.0 OP2 A:A50 4.5 40.8 1.0 OP2 A:G48 4.6 40.0 1.0 OP2 A:A49 4.6 38.2 1.0 C8 A:G48 4.8 42.5 1.0 OP2 A:U47 4.9 40.9 1.0 P A:A50 5.0 41.8 1.0

Magnesium binding site 4 out of 11 in the Thermovirga Lienii 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 Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:45.7 occ:1.00 OP2 A:G98 2.3 54.3 1.0 P A:G98 3.6 52.2 1.0 OP2 A:A31 4.0 46.9 1.0 OP1 A:G98 4.0 46.2 1.0 OP1 A:A31 4.0 45.3 1.0 OP1 A:G30 4.3 48.4 1.0 N4 A:C99 4.6 47.1 1.0 P A:A31 4.6 48.0 1.0 N7 A:G98 4.6 45.2 1.0 O5' A:G98 4.6 45.0 1.0 O3' A:A97 4.6 52.8 1.0 C4' A:A97 4.9 55.1 1.0 C8 A:G98 4.9 44.8 1.0

Magnesium binding site 5 out of 11 in the Thermovirga Lienii C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:38.3 occ:1.00 OP1 A:U6 2.1 40.9 1.0 OP1 A:C71 2.2 45.4 1.0 P A:U6 3.5 39.8 1.0 P A:C71 3.6 40.6 1.0 O3' A:G70 4.1 41.7 1.0 O3' A:C5 4.3 39.9 1.0 OP2 A:U6 4.3 41.5 1.0 OP2 A:G7 4.4 42.5 1.0 O5' A:U6 4.5 41.9 1.0 OP2 A:C71 4.5 39.9 1.0 O5' A:C71 4.6 39.8 1.0 C5' A:C71 4.8 40.6 1.0 C5' A:U6 4.8 41.7 1.0

Magnesium binding site 6 out of 11 in the Thermovirga Lienii C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg208 b:59.5 occ:1.00 OP2 A:A8 4.1 42.5 1.0 OP2 A:G7 4.2 42.5 1.0 N7 A:G7 4.4 47.0 1.0 C8 A:G7 4.6 43.7 1.0 OP2 A:A9 4.7 42.6 1.0 OP2 A:U6 4.8 41.5 1.0 OP1 A:A9 4.8 50.1 1.0 O5' A:G7 5.0 40.5 1.0

Magnesium binding site 7 out of 11 in the Thermovirga Lienii C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg209 b:71.1 occ:1.00 O6 A:G111 4.3 45.2 1.0 N7 A:G111 4.3 48.0 1.0 N4 A:C112 4.6 41.4 1.0 N6 A:A110 4.9 47.0 1.0

Magnesium binding site 8 out of 11 in the Thermovirga Lienii C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:49.4 occ:1.00 N7 A:G122 2.2 46.8 1.0 O6 A:G123 2.3 47.9 1.0 C8 A:G122 3.1 46.6 1.0 C5 A:G122 3.2 45.8 1.0 C6 A:G123 3.3 43.5 1.0 O6 A:G122 3.4 45.6 1.0 C6 A:G122 3.7 45.1 1.0 C5 A:G123 4.0 43.5 1.0 OP2 A:G122 4.1 48.3 1.0 N7 A:G123 4.1 44.4 1.0 N1 A:G123 4.3 41.0 1.0 N7 A:A121 4.3 51.0 1.0 N9 A:G122 4.3 43.7 1.0 C5 A:A121 4.4 50.0 1.0 C4 A:G122 4.4 44.8 1.0 C6 A:A121 4.7 50.1 1.0 C8 A:A121 4.7 52.1 1.0 C4 A:A121 4.8 47.2 1.0 N6 A:A121 4.9 49.2 1.0 N9 A:A121 5.0 48.9 1.0

Magnesium binding site 9 out of 11 in the Thermovirga Lienii C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg211 b:50.2 occ:1.00 OP2 A:G115 2.2 45.5 1.0 OP2 A:U114 2.3 51.0 1.0 P A:G115 3.6 50.0 1.0 P A:U114 3.8 47.7 1.0 O5' A:G115 4.2 47.7 1.0 C3' A:U114 4.4 44.0 1.0 O3' A:U114 4.4 45.9 1.0 O3' A:G113 4.4 45.3 1.0 O5' A:U114 4.5 44.1 1.0 N7 A:G115 4.5 47.3 1.0 C8 A:G115 4.5 45.9 1.0 OP1 A:G115 4.7 49.0 1.0 OP1 A:U114 4.8 46.4 1.0

Magnesium binding site 10 out of 11 in the Thermovirga Lienii C-Di-Amp Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Thermovirga Lienii C-Di-Amp Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg212 b:50.0 occ:1.00 O6 A:G68 4.0 45.9 1.0 N7 A:G68 4.0 47.2 1.0 O6 A:G69 4.1 42.0 1.0 OP2 A:A67 4.2 50.5 1.0 N7 A:G69 4.4 42.9 1.0 C6 A:G68 4.7 43.0 1.0 C5 A:G68 4.7 44.5 1.0 C6 A:G69 4.9 39.9 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