Magnesium in PDB 4znp: The Structure of A Pfi Riboswitch Bound to Zmp

The structure of The Structure of A Pfi Riboswitch Bound to Zmp, PDB code: 4znp was solved by A.Ren, D.J.Patel, R.K.Rajashankar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.20 / 2.94
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.195, 152.195, 86.891, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 24.8

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

Magnesium binding site 1 out of 3 in the The Structure of A Pfi Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of A Pfi Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:70.7 occ:1.00 O A:HOH202 1.9 73.9 1.0 OP1 A:U13 2.1 77.5 1.0 O A:HOH203 2.2 80.5 1.0 O A:HOH201 2.3 69.2 1.0 O5 A:AMZ101 2.3 70.2 1.0 OP2 A:C31 2.4 75.8 1.0 C6 A:AMZ101 3.2 69.5 1.0 P A:C31 3.2 77.4 1.0 O5' A:C31 3.3 75.8 1.0 N2 A:AMZ101 3.4 73.3 1.0 P A:U13 3.5 73.9 1.0 C5' A:C31 3.6 78.0 1.0 OP1 A:C31 3.8 83.6 1.0 OP2 A:U13 4.1 90.0 1.0 N3 A:G67 4.1 79.8 1.0 O2' A:G67 4.2 87.7 1.0 N2 A:G67 4.4 77.2 1.0 O3' A:C12 4.4 78.8 1.0 C3A A:AMZ101 4.5 70.6 1.0 O4' A:G14 4.5 65.4 1.0 O5' A:U13 4.6 66.9 1.0 C1' A:G67 4.6 81.8 1.0 O3' A:A30 4.7 77.1 1.0 C2 A:G67 4.7 78.0 1.0 C1' A:G14 4.7 70.7 1.0 N3 A:AMZ101 4.8 66.8 1.0 C5' A:U13 4.9 72.2 1.0 C2' A:G67 4.9 85.3 1.0

Magnesium binding site 2 out of 3 in the The Structure of A Pfi Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of A Pfi Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:87.9 occ:1.00 O A:HOH205 2.0 79.8 1.0 O A:HOH204 2.6 84.9 1.0 OP1 A:G23 3.4 93.5 1.0 O2' A:A22 3.5 80.2 1.0 C2' A:A22 4.4 77.5 1.0 O6 A:G18 4.5 77.7 1.0 P A:G23 4.6 99.0 1.0 C3' A:A22 4.8 80.2 1.0 N7 A:G18 4.9 80.9 1.0

Magnesium binding site 3 out of 3 in the The Structure of A Pfi Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of A Pfi Riboswitch Bound to Zmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:0.5 occ:1.00 OP2 B:C31 2.0 1.0 1.0 OP1 B:U13 2.1 0.4 1.0 O5 B:AMZ101 2.5 0.6 1.0 P B:C31 3.2 1.0 1.0 C6 B:AMZ101 3.2 0.3 1.0 N2 B:AMZ101 3.3 0.8 1.0 P B:U13 3.5 0.3 1.0 C5' B:C31 3.5 0.1 1.0 O5' B:C31 3.6 0.1 1.0 OP1 B:C31 3.9 0.3 1.0 O2' B:G67 4.2 0.3 1.0 OP2 B:U13 4.3 0.9 1.0 O3' B:C12 4.4 0.2 1.0 O5' B:U13 4.4 0.0 1.0 O3' B:A30 4.5 0.6 1.0 N3 B:G67 4.6 0.5 1.0 O4' B:G14 4.6 0.5 1.0 C3A B:AMZ101 4.7 0.6 1.0 N2 B:G67 4.8 0.6 1.0

A.Ren, K.R.Rajashankar, D.J.Patel. Global Rna Fold and Molecular Recognition For A Pfl Riboswitch Bound to Zmp, A Master Regulator of One-Carbon Metabolism. Structure V. 23 1375 2015.
ISSN: ISSN 0969-2126
PubMed: 26118534
DOI: 10.1016/J.STR.2015.05.016