Magnesium in PDB 8hzj: A New Fluorescent Rna Aptamer Bound with N571

The structure of A New Fluorescent Rna Aptamer Bound with N571, PDB code: 8hzj was solved by K.Y.Huang, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.37 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.316, 48.173, 58.304, 90, 116.03, 90
R / Rfree (%)	18.8 / 25.9

The structure of A New Fluorescent Rna Aptamer Bound with N571 also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Potassium	(K)	2 atoms

The binding sites of Magnesium atom in the A New Fluorescent Rna Aptamer Bound with N571 (pdb code 8hzj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the A New Fluorescent Rna Aptamer Bound with N571, PDB code: 8hzj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the A New Fluorescent Rna Aptamer Bound with N571


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A New Fluorescent Rna Aptamer Bound with N571 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:37.2 occ:1.00 O B:HOH214 2.2 41.5 1.0 O A:HOH208 2.3 36.8 1.0 O B:HOH212 2.4 31.1 1.0 O B:HOH201 2.6 32.5 1.0 OP1 B:G25 3.2 35.9 1.0 C2 A:A23 3.3 26.5 1.0 N1 A:A23 3.7 27.4 1.0 N1 A:A22 4.1 30.5 1.0 P B:G25 4.2 34.9 1.0 N3 A:A23 4.3 29.4 1.0 OP2 B:G25 4.4 39.5 1.0 N6 A:A22 4.7 29.3 1.0 OP2 B:C26 4.7 29.6 1.0 O B:HOH216 4.8 33.6 1.0 O5' B:G25 4.8 36.6 1.0 C6 A:A22 4.9 31.6 1.0 C2 A:A22 4.9 30.8 1.0

Magnesium binding site 2 out of 6 in the A New Fluorescent Rna Aptamer Bound with N571


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A New Fluorescent Rna Aptamer Bound with N571 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:45.9 occ:1.00 OP1 A:G25 3.8 32.9 1.0 N1 B:A23 4.0 30.7 1.0 C2 B:A23 4.0 32.9 1.0 OP2 A:G9 4.2 39.8 1.0 O A:HOH213 4.3 37.1 1.0 OP2 A:C26 4.3 34.2 1.0 OP2 A:G25 4.4 35.0 1.0 P A:G25 4.5 31.1 1.0 N1 B:A22 4.6 33.9 1.0 O5' A:G25 4.7 27.6 1.0 OP1 A:G9 5.0 27.4 1.0

Magnesium binding site 3 out of 6 in the A New Fluorescent Rna Aptamer Bound with N571


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A New Fluorescent Rna Aptamer Bound with N571 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:33.8 occ:1.00 O A:HOH213 2.3 37.1 1.0 O A:HOH211 2.4 36.0 1.0 O A:HOH204 2.5 23.8 1.0 O A:HOH210 2.6 30.5 1.0 O A:HOH209 2.7 34.2 1.0 O A:HOH206 2.7 38.2 1.0 N7 A:A27 3.4 31.6 1.0 C8 A:A27 3.9 32.6 1.0 O6 A:G28 4.0 31.8 1.0 C5 A:C26 4.2 28.0 1.0 N7 A:G28 4.3 28.8 1.0 C4 A:C26 4.6 27.5 1.0 C5 A:A27 4.6 27.5 1.0 OP2 A:C26 4.6 34.2 1.0 N4 A:C26 4.7 26.2 1.0 OP2 A:A27 4.7 36.6 1.0 C6 A:G28 4.7 27.4 1.0 C6 A:C26 4.8 31.4 1.0 C5 A:G28 4.8 26.4 1.0 N6 A:A27 5.0 29.4 1.0

Magnesium binding site 4 out of 6 in the A New Fluorescent Rna Aptamer Bound with N571


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A New Fluorescent Rna Aptamer Bound with N571 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:44.6 occ:1.00 OP2 A:G20 2.2 32.8 1.0 P A:G20 3.6 31.6 1.0 OP1 A:C19 3.8 49.4 1.0 OP2 A:C19 3.8 28.2 1.0 P A:C19 4.1 38.2 1.0 O5' A:C19 4.2 36.4 1.0 OP1 A:G20 4.3 26.4 1.0 O3' A:C19 4.5 34.2 1.0 O5' A:G20 4.5 30.2 1.0 C3' A:C19 4.8 33.3 1.0 C5' A:C19 4.9 34.0 1.0

Magnesium binding site 5 out of 6 in the A New Fluorescent Rna Aptamer Bound with N571


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A New Fluorescent Rna Aptamer Bound with N571 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:34.8 occ:1.00 O B:HOH210 1.9 39.1 1.0 O B:HOH213 2.2 32.7 1.0 O B:HOH208 2.2 30.6 1.0 O B:HOH204 2.2 32.8 1.0 O B:HOH216 2.3 33.6 1.0 O B:HOH209 2.6 34.9 1.0 N7 B:A27 4.1 33.2 1.0 N7 B:G28 4.1 33.1 1.0 O6 B:G28 4.2 30.6 1.0 OP2 B:A27 4.3 28.6 1.0 O2' B:U8 4.5 31.2 1.0 C8 B:A27 4.6 30.4 1.0 OP2 B:U8 4.7 33.4 1.0 OP2 B:C26 4.7 29.6 1.0 C2' B:U8 4.8 34.6 1.0 C5 B:G28 4.9 32.2 1.0 C6 B:G28 4.9 31.2 1.0

Magnesium binding site 6 out of 6 in the A New Fluorescent Rna Aptamer Bound with N571


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A New Fluorescent Rna Aptamer Bound with N571 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:43.0 occ:1.00 O B:HOH203 2.1 42.2 1.0 OP2 B:A31 2.4 41.1 1.0 OP2 B:C30 3.1 37.0 1.0 P B:A31 3.8 40.1 1.0 P B:C30 4.5 41.4 1.0 OP1 B:A31 4.5 35.0 1.0 O5' B:A31 4.7 37.5 1.0 O3' B:C30 4.7 37.9 1.0 O5' B:C30 4.8 34.5 1.0 N7 B:A31 4.9 42.7 1.0

K.Huang, Q.Song, M.Fang, D.Yao, X.Shen, X.Xu, X.Chen, L.Zhu, Y.Yang, A.Ren. Structural Basis of A Small Monomeric Clivia Fluorogenic Rna with A Large Stokes Shift. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38816645
DOI: 10.1038/S41589-024-01633-1