Magnesium in PDB 8hzd: A New Fluorescent Rna Aptamer Bound with N618

The structure of A New Fluorescent Rna Aptamer Bound with N618, PDB code: 8hzd was solved by Q.Q.Song, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.16 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.494, 46.461, 56.251, 90, 113.81, 90
R / Rfree (%)	21.1 / 25.9

The structure of A New Fluorescent Rna Aptamer Bound with N618 also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the A New Fluorescent Rna Aptamer Bound with N618 (pdb code 8hzd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the A New Fluorescent Rna Aptamer Bound with N618, PDB code: 8hzd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:32.7 occ:1.00 O A:HOH220 2.0 38.7 1.0 O A:HOH212 2.1 32.1 1.0 O A:HOH207 2.2 28.8 1.0 O A:HOH241 2.3 42.3 1.0 O A:HOH205 2.3 32.6 1.0 O A:HOH229 2.3 33.3 1.0 O A:HOH240 4.1 36.4 1.0 N7 A:A27 4.1 33.5 1.0 OP2 A:A27 4.1 33.2 1.0 OP2 A:C26 4.1 33.5 1.0 O6 A:G28 4.2 33.9 1.0 O A:HOH218 4.3 32.7 1.0 N7 A:G28 4.4 34.6 1.0 N26 A:O2I104 4.4 35.1 1.0 O2' A:U8 4.4 28.2 1.0 O A:HOH219 4.4 34.8 1.0 C8 A:A27 4.5 35.3 1.0 OP2 A:U8 4.6 38.0 1.0 C2' A:U8 4.7 27.3 1.0 C25 A:O2I104 4.8 33.9 1.0 C5 A:C26 4.9 27.9 1.0 C6 A:G28 5.0 35.6 1.0

Magnesium binding site 2 out of 7 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:35.2 occ:1.00 OP2 A:G20 1.9 36.5 1.0 O A:HOH236 2.0 34.2 1.0 O A:HOH216 2.1 37.1 1.0 O A:HOH232 2.1 35.9 1.0 O A:HOH231 2.1 40.7 1.0 P A:G20 3.3 34.4 1.0 O5' A:G20 3.7 36.7 1.0 O A:HOH217 4.1 33.2 1.0 OP2 A:C19 4.2 37.9 1.0 N7 A:G20 4.2 32.6 1.0 O5' A:C19 4.2 41.2 1.0 OP1 A:G20 4.3 31.6 1.0 C8 A:G20 4.3 30.9 1.0 O3' A:C19 4.3 29.7 1.0 C3' A:C19 4.5 34.5 1.0 OP2 A:A21 4.5 37.3 1.0 P A:C19 4.5 41.5 1.0 OP1 A:C19 4.6 43.6 1.0

Magnesium binding site 3 out of 7 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:45.8 occ:1.00 O2' A:C36 1.9 51.5 1.0 O3' A:C36 2.1 42.4 1.0 C2' A:C36 2.8 47.4 1.0 C3' A:C36 2.9 43.2 1.0 C4' A:C36 3.6 45.2 1.0 C1' A:C36 4.0 42.0 1.0 O4' A:C36 4.4 44.7 1.0 C5' A:C36 4.8 46.5 1.0

Magnesium binding site 4 out of 7 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:28.7 occ:1.00 O B:HOH225 1.9 27.4 1.0 O B:HOH239 1.9 37.1 1.0 O A:HOH233 2.0 39.8 1.0 O B:HOH241 2.1 35.7 1.0 O B:HOH233 2.1 25.1 1.0 O A:HOH223 2.2 31.2 1.0 OP1 B:G25 4.2 27.6 1.0 O B:HOH229 4.2 35.6 1.0 OP2 B:C26 4.3 25.1 1.0 C2 A:A23 4.4 29.6 1.0 N1 A:A22 4.4 33.8 1.0 O B:HOH221 4.4 34.0 1.0 N1 A:A23 4.5 29.4 1.0 OP2 B:G9 4.6 32.7 1.0 N6 A:A22 4.8 31.8 1.0 P B:G25 4.9 28.2 1.0 OP2 B:G25 5.0 29.4 1.0

Magnesium binding site 5 out of 7 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:61.9 occ:1.00 O2' B:C36 2.0 58.0 1.0 O3' B:C36 2.6 58.0 1.0 C2' B:C36 2.8 55.7 1.0 C3' B:C36 3.2 54.1 0.0 C4' B:C36 4.2 54.7 1.0 C1' B:C36 4.2 56.2 1.0 O4' B:C36 4.8 51.6 1.0

Magnesium binding site 6 out of 7 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:35.8 occ:1.00 O B:HOH237 2.0 28.5 1.0 O B:HOH214 2.5 33.3 1.0 N7 B:A27 3.0 31.4 1.0 O B:HOH235 3.2 38.4 1.0 O6 B:G28 3.6 32.9 1.0 C8 B:A27 3.8 30.2 1.0 C5 B:C26 3.9 25.7 1.0 N7 B:G28 4.1 24.3 1.0 C5 B:A27 4.2 28.9 1.0 C4 B:C26 4.2 28.4 1.0 OP2 B:A27 4.3 30.4 1.0 N4 B:C26 4.3 29.7 1.0 C6 B:G28 4.3 27.6 1.0 N6 B:A27 4.4 29.1 1.0 C6 B:C26 4.5 24.6 1.0 C5 B:G28 4.6 28.1 1.0 OP2 B:C26 4.7 25.1 1.0 C6 B:A27 4.7 29.5 1.0 N3 B:C26 5.0 26.6 1.0

Magnesium binding site 7 out of 7 in the A New Fluorescent Rna Aptamer Bound with N618


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of A New Fluorescent Rna Aptamer Bound with N618 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:42.8 occ:1.00 OP2 B:A31 2.0 36.4 1.0 OP2 B:C30 2.1 33.8 1.0 O B:HOH219 2.1 36.9 1.0 P B:C30 3.4 28.1 1.0 P B:A31 3.4 33.7 1.0 O5' B:C30 3.8 28.7 1.0 C5' B:C30 3.8 31.8 1.0 O B:HOH218 4.1 34.1 1.0 N7 B:A31 4.2 30.6 1.0 OP1 B:A31 4.2 40.4 1.0 O3' B:C30 4.3 34.6 1.0 O5' B:A31 4.3 35.4 1.0 OP1 B:C30 4.4 23.4 1.0 O3' B:A29 4.4 28.2 1.0 C8 B:A31 4.5 33.2 1.0 C3' B:C30 4.5 34.1 1.0 C4' B:C30 4.7 30.0 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