Magnesium in PDB 4tzy: Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+

The structure of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+, PDB code: 4tzy was solved by J.Zhang, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.38 / 2.57
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.283, 152.313, 24.995, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.1

The structure of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ also contains other interesting chemical elements:

Strontium

(Sr)

7 atoms

The binding sites of Magnesium atom in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ (pdb code 4tzy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+, PDB code: 4tzy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg107 b:32.0 occ:1.00 O2' X:G38 3.0 49.8 1.0 N2 X:G32 3.4 46.1 1.0 N1 X:G32 3.4 46.0 1.0 N6 X:A33 3.4 35.2 1.0 C6 X:A33 3.6 36.0 1.0 N1 X:A33 3.9 36.9 1.0 C2 X:G32 3.9 45.7 1.0 N7 X:A66 4.0 42.9 1.0 C5 X:A33 4.3 38.1 1.0 C2' X:G38 4.4 47.2 1.0 C6 X:G32 4.5 38.7 1.0 O6 X:G32 4.6 34.5 1.0 C5 X:A66 4.6 52.2 1.0 C8 X:A66 4.6 42.1 1.0 C5 X:U39 4.7 42.6 1.0 C2 X:A33 4.7 37.9 1.0 OP2 X:C67 4.7 43.2 1.0 N6 X:A66 4.8 52.8 1.0 C1' X:G38 4.8 45.9 1.0 N7 X:A33 4.8 38.0 1.0 C4' X:G38 4.8 45.6 1.0 O3' X:G38 4.9 44.2 1.0 C6 X:A66 4.9 52.4 1.0 C4 X:A33 5.0 37.2 1.0 C3' X:G38 5.0 43.6 1.0

Magnesium binding site 2 out of 2 in the Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vibrio Vulnificus Adenine Riboswitch Variant, Grown in Both SR2+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg108 b:99.2 occ:1.00 OP2 X:U22 2.6 47.2 1.0 OP1 X:A21 2.9 56.3 1.0 P X:U22 3.7 42.2 1.0 OP1 X:U22 4.0 42.4 1.0 P X:A21 4.0 54.7 1.0 O5' X:A21 4.3 39.1 1.0 C5' X:A21 4.5 37.8 1.0 OP2 X:A21 4.6 55.4 1.0 O3' X:A21 4.6 42.6 1.0 O5' X:U22 5.0 31.2 1.0

J.Zhang, A.R.Ferre-D'amare. Dramatic Improvement of Crystals of Large Rnas By Cation Replacement and Dehydration. Structure V. 22 1363 2014.
ISSN: ISSN 0969-2126
PubMed: 25185828
DOI: 10.1016/J.STR.2014.07.011