Magnesium in PDB 8hzf: A New Fluorescent Rna Aptamer Bound with N565

The structure of A New Fluorescent Rna Aptamer Bound with N565, PDB code: 8hzf 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)	40.20 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.634, 47.237, 56.17, 90, 115.26, 90
R / Rfree (%)	18.2 / 25.6

The structure of A New Fluorescent Rna Aptamer Bound with N565 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 N565 (pdb code 8hzf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A New Fluorescent Rna Aptamer Bound with N565, PDB code: 8hzf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the A New Fluorescent Rna Aptamer Bound with N565


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 N565 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:44.1 occ:1.00 O A:HOH203 2.3 53.3 1.0 OP2 A:G20 2.5 51.3 1.0 P A:G20 4.0 49.3 1.0 OP2 A:C19 4.3 49.2 1.0 O5' A:C19 4.4 52.1 1.0 O5' A:G20 4.5 49.4 1.0 N7 A:G20 4.7 46.4 1.0 P A:C19 4.8 57.4 1.0 OP1 A:G20 4.8 52.2 1.0 C8 A:G20 4.9 46.8 1.0 O3' A:C19 4.9 46.1 1.0 OP2 A:A21 5.0 47.0 1.0 OP1 A:C19 5.0 55.8 1.0

Magnesium binding site 2 out of 4 in the A New Fluorescent Rna Aptamer Bound with N565


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 N565 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:45.4 occ:1.00 O A:HOH202 1.9 40.8 1.0 O B:HOH207 2.1 44.2 1.0 O B:HOH203 2.1 42.9 1.0 O B:HOH204 2.2 53.1 1.0 O B:HOH208 2.7 44.3 1.0 OP1 B:G25 3.8 51.9 1.0 C2 A:A23 3.9 42.1 1.0 N1 A:A23 4.1 40.3 1.0 N1 A:A22 4.1 34.0 1.0 OP2 B:C26 4.4 42.6 1.0 N6 A:A22 4.5 46.9 1.0 OP2 B:G9 4.8 49.6 1.0 C6 A:A22 4.8 42.4 1.0 P B:G25 4.8 49.0 1.0 OP1 B:G9 4.9 51.9 1.0 OP2 B:G25 5.0 44.9 1.0 N3 A:A23 5.0 38.5 1.0

Magnesium binding site 3 out of 4 in the A New Fluorescent Rna Aptamer Bound with N565


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 N565 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:62.4 occ:1.00 OP2 B:G20 2.2 51.2 1.0 O B:HOH205 2.4 44.8 1.0 P B:G20 3.5 51.2 1.0 OP1 B:G20 4.2 54.3 1.0 O5' B:G20 4.3 46.9 1.0 OP2 B:A21 4.4 46.5 1.0 OP2 B:C19 4.5 57.4 1.0 O3' B:C19 4.7 44.1 1.0 OP1 B:C19 5.0 56.4 1.0

Magnesium binding site 4 out of 4 in the A New Fluorescent Rna Aptamer Bound with N565


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 N565 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:40.9 occ:1.00 OP2 B:A31 2.2 41.4 1.0 OP2 B:C30 2.6 49.3 1.0 P B:A31 3.6 55.0 1.0 P B:C30 3.9 49.1 1.0 O5' B:C30 4.1 45.6 1.0 N7 B:A31 4.3 61.4 1.0 OP1 B:A31 4.3 60.4 1.0 O5' B:A31 4.4 54.0 1.0 C5' B:C30 4.6 40.7 1.0 C8 B:A31 4.6 55.2 1.0 O3' B:A29 4.8 51.9 1.0 O3' B:C30 4.8 45.3 1.0 OP1 B:C30 4.9 49.4 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