Magnesium in PDB 4xw7: Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom

The structure of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom, PDB code: 4xw7 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)	25.57 / 2.50
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 (%)	25 / 27.4

The structure of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom also contains other interesting chemical elements:

Iridium

(Ir)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom (pdb code 4xw7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom, PDB code: 4xw7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 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 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:26.1 occ:1.00 OP1 A:U11 2.0 23.3 1.0 OP2 A:C29 2.1 27.4 1.0 O A:HOH401 2.3 24.8 1.0 O5 A:AMZ101 2.8 26.2 1.0 P A:U11 3.4 23.5 1.0 P A:C29 3.4 29.0 1.0 C6 A:AMZ101 3.8 24.9 1.0 O5' A:C29 3.9 33.1 1.0 N2 A:AMZ101 3.9 25.9 1.0 C5' A:C29 3.9 34.1 1.0 OP2 A:U11 4.1 24.9 1.0 OP1 A:C29 4.2 28.2 1.0 O5' A:U11 4.3 23.2 1.0 O3' A:C10 4.4 23.1 1.0 O3' A:A28 4.6 29.5 1.0

Magnesium binding site 2 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 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 2.50 Angstrom within 5.0Å range:

Magnesium binding site 3 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 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 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:46.5 occ:1.00 OP2 A:G2 3.3 44.6 1.0 MG A:MG105 3.3 46.3 1.0 P A:G2 4.3 43.3 1.0 OP1 A:G2 4.4 42.7 1.0 OP1 A:G39 4.8 30.6 1.0 OP2 A:G39 4.9 28.7 1.0 P A:G1 5.0 61.3 1.0

Magnesium binding site 4 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:46.3 occ:1.00 OP1 A:G39 2.8 30.6 1.0 MG A:MG104 3.3 46.5 1.0 P A:G39 3.7 26.7 1.0 O3' A:A38 4.0 26.3 1.0 OP2 A:G39 4.0 28.7 1.0

Magnesium binding site 5 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:31.5 occ:1.00 OP1 A:C18 3.3 25.4 1.0 O3' A:A17 3.9 25.6 1.0 P A:C18 4.2 24.3 1.0 O5' A:C18 4.5 23.9 1.0 O2' A:A17 4.6 23.4 1.0

Magnesium binding site 6 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:33.2 occ:1.00 O A:HOH416 2.1 37.6 1.0 O A:HOH417 2.1 34.2 1.0 O A:HOH415 2.8 35.5 1.0 O6 A:G25 4.6 46.2 1.0 N7 A:G23 4.7 34.0 1.0 O6 A:G23 4.9 36.4 1.0

Magnesium binding site 7 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:34.2 occ:1.00 OP2 A:G21 3.0 29.2 1.0 MG A:MG109 3.1 30.1 1.0 N7 A:G21 3.9 28.6 1.0 OP2 A:G13 4.1 23.3 1.0 C3' A:G20 4.2 26.3 1.0 P A:G21 4.3 27.0 1.0 C8 A:G20 4.3 25.9 1.0 C8 A:G21 4.3 28.2 1.0 N7 A:G20 4.4 26.6 1.0 O3' A:G20 4.7 26.9 1.0 C5' A:G20 4.7 26.2 1.0 O5' A:G21 4.8 27.4 1.0 N9 A:G20 4.8 26.2 1.0 C5 A:G20 4.9 26.2 1.0 C4' A:G20 5.0 26.0 1.0

Magnesium binding site 8 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:30.1 occ:1.00 O6 A:G21 2.6 29.9 1.0 N7 A:G21 2.9 28.6 1.0 MG A:MG108 3.1 34.2 1.0 C6 A:G21 3.3 29.8 1.0 C5 A:G21 3.4 29.2 1.0 O4 A:U22 3.7 32.4 1.0 O6 A:G20 4.1 27.1 1.0 C8 A:G21 4.2 28.2 1.0 C6 A:G20 4.2 26.9 1.0 N7 A:G20 4.2 26.6 1.0 C5 A:G20 4.3 26.2 1.0 C4 A:U22 4.6 31.8 1.0 N6 A:A31 4.6 32.6 1.0 N1 A:G21 4.7 30.0 1.0 C4 A:G21 4.8 28.9 1.0 OP2 A:G13 4.9 23.3 1.0 C5 A:U22 4.9 31.4 1.0 C8 A:G20 5.0 25.9 1.0 N1 A:G20 5.0 26.8 1.0

Magnesium binding site 9 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:49.0 occ:1.00 N7 A:G25 4.2 44.8 1.0 OP2 A:G24 4.3 45.8 1.0 O A:HOH416 4.6 37.6 1.0 O6 A:G25 4.6 46.2 1.0 N6 A:A26 4.8 50.1 1.0

Magnesium binding site 10 out of 13 in the Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Zmp Riboswitch at 2.50 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:28.6 occ:1.00 O4' A:A19 2.9 25.0 1.0 O5' A:A19 3.2 25.0 1.0 O2' A:G20 3.3 25.8 1.0 C4' A:A19 3.7 25.2 1.0 C1' A:A19 4.0 25.6 1.0 O4' A:G20 4.0 25.9 1.0 C5' A:A19 4.1 24.8 1.0 OP2 A:A19 4.1 24.7 1.0 C4' A:G20 4.2 26.0 1.0 N9 A:A19 4.2 24.4 1.0 C1' A:G20 4.2 25.4 1.0 P A:A19 4.3 23.6 1.0 C2' A:G20 4.3 26.3 1.0 C4 A:A19 4.5 25.6 1.0 N3 A:A19 4.6 25.6 1.0 O2' A:C18 4.7 24.0 1.0 O3' A:C18 4.7 24.6 1.0 C8 A:A19 4.8 25.9 1.0 C3' A:G20 4.8 26.3 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