Magnesium in PDB 4xwf: Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom

The structure of Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom, PDB code: 4xwf was solved by J.J.Trausch, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.75 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	40.160, 40.160, 234.910, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.9

The structure of Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom also contains other interesting chemical elements:

Arsenic	(As)	1 atom
Iridium	(Ir)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom (pdb code 4xwf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom, PDB code: 4xwf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom


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 the Zmp Riboswitch at 1.80 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:25.8 occ:1.00 O A:HOH221 1.9 28.3 1.0 OP1 A:U11 2.0 25.1 1.0 O A:HOH225 2.0 24.8 1.0 OP2 A:C29 2.0 32.1 1.0 O A:HOH222 2.1 24.4 1.0 O5 A:AMZ101 2.2 25.3 1.0 C6 A:AMZ101 3.2 21.6 1.0 P A:U11 3.3 24.0 1.0 N2 A:AMZ101 3.4 25.1 1.0 P A:C29 3.5 32.9 1.0 O5' A:U11 3.9 27.7 1.0 OP2 A:U11 3.9 23.0 1.0 C5' A:C29 4.0 29.9 1.0 O5' A:C29 4.1 28.6 1.0 O4' A:G12 4.3 25.3 1.0 OP1 A:C29 4.3 37.6 1.0 O3' A:A28 4.4 43.0 1.0 O3' A:C10 4.4 20.1 1.0 C3A A:AMZ101 4.5 20.7 1.0 C5' A:U11 4.5 25.6 1.0 C1' A:G12 4.6 18.3 1.0 N3 A:AMZ101 4.8 21.3 1.0 O A:HOH230 5.0 49.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom


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 the Zmp Riboswitch at 1.80 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:22.2 occ:1.00 O A:HOH228 1.9 24.5 1.0 O A:HOH231 1.9 21.6 1.0 O2 A:C52 2.0 18.9 1.0 O A:HOH237 2.0 20.9 1.0 O A:HOH214 2.3 28.4 1.0 C2 A:C52 3.0 29.7 1.0 N3 A:C52 3.4 20.4 1.0 OP2 A:G55 3.9 33.8 1.0 O A:HOH249 4.1 38.4 1.0 N1 A:C52 4.2 23.7 1.0 N4 A:C56 4.4 24.2 1.0 O A:HOH229 4.4 21.0 1.0 N7 A:G55 4.4 25.8 1.0 OP2 A:C54 4.4 28.9 1.0 C1' A:C52 4.5 23.2 1.0 C4 A:C52 4.8 29.0 1.0 C5 A:C54 4.8 21.2 1.0 C8 A:G55 5.0 35.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Zmp Riboswitch at 1.80 Angstrom


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 the Zmp Riboswitch at 1.80 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:37.4 occ:1.00 O6 A:G23 2.2 24.3 1.0 O1 A:CAC109 2.3 32.7 0.9 O4 A:U22 2.4 32.1 1.0 O A:HOH278 2.6 32.4 1.0 O2 A:CAC109 2.7 34.9 0.9 O A:HOH255 2.8 30.0 1.0 AS A:CAC109 3.0 83.3 0.9 C4 A:U22 3.2 27.4 1.0 C6 A:G23 3.2 34.8 1.0 N7 A:G23 3.7 37.8 1.0 C5 A:U22 3.8 28.3 1.0 C5 A:G23 3.8 36.8 1.0 N4 A:C30 4.0 26.9 1.0 C2 A:CAC109 4.0 31.1 0.9 N6 A:A31 4.1 27.3 1.0 O6 A:G24 4.1 33.7 1.0 O A:HOH256 4.1 34.3 1.0 N3 A:U22 4.2 31.1 1.0 N1 A:G23 4.5 31.6 1.0 O A:HOH283 4.5 39.7 1.0 OP1 A:G13 4.6 24.3 1.0 C6 A:G24 4.7 36.4 1.0 C1 A:CAC109 4.7 46.0 0.9 N4 A:C29 4.7 34.3 1.0 N7 A:G24 4.8 37.2 1.0 C6 A:U22 5.0 31.6 1.0 C6 A:A31 5.0 29.1 1.0 C5 A:G24 5.0 38.9 1.0

J.J.Trausch, J.G.Marcano-Velazquez, M.M.Matyjasik, R.T.Batey. Metal Ion-Mediated Nucleobase Recognition By the Ztp Riboswitch. Chem.Biol. V. 22 829 2015.
ISSN: ISSN 1074-5521
PubMed: 26144884
DOI: 10.1016/J.CHEMBIOL.2015.06.007