Magnesium in PDB 4kqy: Bacillus Subtilis Yitj S Box/Sam-I Riboswitch

The structure of Bacillus Subtilis Yitj S Box/Sam-I Riboswitch, PDB code: 4kqy was solved by C.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.68 / 3.02
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.732, 58.732, 204.091, 90.00, 90.00, 120.00
R / Rfree (%)	23.7 / 30

The binding sites of Magnesium atom in the Bacillus Subtilis Yitj S Box/Sam-I Riboswitch (pdb code 4kqy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bacillus Subtilis Yitj S Box/Sam-I Riboswitch, PDB code: 4kqy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bacillus Subtilis Yitj S Box/Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacillus Subtilis Yitj S Box/Sam-I Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:4.7 occ:1.00 OP2 A:A10 2.2 21.1 1.0 OP2 A:U85 2.3 24.0 1.0 P A:A10 3.2 22.4 1.0 P A:U85 3.2 24.3 1.0 OP1 A:U85 3.4 24.1 1.0 O5' A:A10 3.6 20.4 1.0 OP1 A:A10 3.6 21.6 1.0 O3' A:A84 3.9 27.9 1.0 C4' A:A84 4.1 29.4 1.0 N7 A:G11 4.2 18.6 1.0 C3' A:A84 4.2 29.4 1.0 N7 A:A10 4.4 16.4 1.0 C5' A:A84 4.4 28.6 1.0 C8 A:A10 4.4 16.7 1.0 OP1 A:A83 4.4 20.4 1.0 O3' A:A9 4.6 23.7 1.0 O5' A:U85 4.7 22.2 1.0 O6 A:G11 4.7 16.5 1.0 OP2 A:G11 4.9 22.7 1.0 C5' A:A10 4.9 19.9 1.0

Magnesium binding site 2 out of 2 in the Bacillus Subtilis Yitj S Box/Sam-I Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacillus Subtilis Yitj S Box/Sam-I Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:31.2 occ:1.00 OP1 A:C25 2.5 62.9 1.0 OP2 A:G23 2.7 39.2 1.0 P A:C25 3.7 58.6 1.0 O3' A:A24 3.7 44.7 1.0 P A:G23 4.1 39.5 1.0 OP1 A:G23 4.5 41.2 1.0 OP2 A:C25 4.7 52.3 1.0 OP1 A:G22 4.8 58.4 1.0 O5' A:C25 4.8 58.9 1.0 O5' A:G22 4.9 53.8 1.0 C3' A:A24 5.0 38.2 1.0 O3' A:G22 5.0 40.1 1.0

C.Lu, F.Ding, A.Chowdhury, V.Pradhan, J.Tomsic, W.M.Holmes, T.M.Henkin, A.Ke. Sam Recognition and Conformational Switching Mechanism in the Bacillus Subtilis Yitj S Box/Sam-I Riboswitch J.Mol.Biol. V. 404 803 2010.
ISSN: ISSN 0022-2836
PubMed: 20951706
DOI: 10.1016/J.JMB.2010.09.059