Magnesium in PDB 3irw: Structure of A C-Di-Gmp Riboswitch From V. Cholerae

The structure of Structure of A C-Di-Gmp Riboswitch From V. Cholerae, PDB code: 3irw was solved by K.D.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.69 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.461, 45.123, 76.573, 90.00, 96.79, 90.00
R / Rfree (%)	19.6 / 25.1

The structure of Structure of A C-Di-Gmp Riboswitch From V. Cholerae also contains other interesting chemical elements:

Iridium

(Ir)

9 atoms

The binding sites of Magnesium atom in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae (pdb code 3irw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae, PDB code: 3irw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg673 b:61.9 occ:1.00 O2 R:C22 2.2 35.6 1.0 O2' R:A49 2.4 22.1 1.0 O2' R:C22 2.8 40.2 1.0 O3' R:A49 3.1 24.9 1.0 C2' R:C22 3.2 35.1 1.0 N2 R:G45 3.3 39.6 1.0 C2 R:C22 3.3 34.3 1.0 O4' R:A23 3.4 34.1 1.0 C2' R:A49 3.4 22.6 1.0 C1' R:A49 3.5 23.3 1.0 C1' R:C22 3.6 33.8 1.0 C3' R:A49 3.8 22.6 1.0 C4' R:A23 3.9 35.7 1.0 N1 R:C22 3.9 35.0 1.0 N3 R:A49 4.1 28.4 1.0 N7 R:G83 4.1 20.2 1.0 P R:G50 4.1 26.4 1.0 OP2 R:G50 4.2 24.7 1.0 O6 R:G83 4.2 25.1 1.0 C5' R:A23 4.3 34.8 1.0 N3 R:C22 4.4 34.4 1.0 O4' R:A49 4.4 24.5 1.0 C1' R:A23 4.5 33.0 1.0 C2 R:G45 4.6 34.6 1.0 N9 R:A49 4.6 27.1 1.0 OP1 R:G50 4.6 28.6 1.0 O2 R:C46 4.7 36.2 1.0 C3' R:C22 4.7 33.9 1.0 C4' R:A49 4.7 22.8 1.0 C4 R:A49 4.7 28.2 1.0 C5 R:G83 4.8 19.9 1.0 C6 R:G83 4.8 19.7 1.0 O R:HOH123 4.9 62.1 1.0 N2 R:G21 4.9 49.8 1.0 O4' R:C22 4.9 34.4 1.0

Magnesium binding site 2 out of 2 in the Structure of A C-Di-Gmp Riboswitch From V. Cholerae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A C-Di-Gmp Riboswitch From V. Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg674 b:80.3 occ:1.00 O21 R:C2E1 2.4 27.9 1.0 O R:HOH111 2.5 36.5 1.0 OP2 R:C15 3.0 45.8 1.0 P11 R:C2E1 3.9 25.3 1.0 O11 R:C2E1 4.2 27.1 1.0 P R:C15 4.3 45.4 1.0 O3' R:G14 4.6 56.9 1.0 O2' R:G14 4.7 50.5 1.0 C3' R:G14 4.8 52.5 1.0 O5A R:C2E1 4.8 28.4 1.0 C5A R:C2E1 4.9 29.5 1.0 OP2 R:A16 4.9 34.9 1.0 O3' R:C2E1 5.0 28.2 1.0

K.D.Smith, S.V.Lipchock, T.D.Ames, J.Wang, R.R.Breaker, S.A.Strobel. Structural Basis of Ligand Binding By A C-Di-Gmp Riboswitch. Nat.Struct.Mol.Biol. V. 16 1218 2009.
ISSN: ISSN 1545-9993
PubMed: 19898477
DOI: 10.1038/NSMB.1702