Magnesium in PDB 8hze: A New Fluorescent Rna Aptamer Bound with N

The structure of A New Fluorescent Rna Aptamer Bound with N, PDB code: 8hze 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)	38.19 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.151, 45.87, 57.116, 90, 115.08, 90
R / Rfree (%)	20 / 23.4

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

Potassium

(K)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the A New Fluorescent Rna Aptamer Bound with N (pdb code 8hze). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the A New Fluorescent Rna Aptamer Bound with N, PDB code: 8hze:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


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 N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:27.0 occ:1.00 O A:HOH220 2.0 30.8 1.0 O A:HOH214 2.1 30.2 1.0 O A:HOH255 2.1 31.1 1.0 O A:HOH256 2.1 36.1 1.0 O A:HOH242 2.1 32.2 1.0 O A:HOH231 2.2 26.9 1.0 O A:HOH251 3.8 36.9 1.0 OP2 A:A27 3.9 30.5 1.0 O A:HOH246 4.1 35.0 1.0 N7 A:A27 4.3 25.8 1.0 O6 A:G28 4.3 26.3 1.0 O2' A:U8 4.3 25.8 1.0 O A:HOH233 4.3 36.1 1.0 O A:HOH240 4.3 32.5 1.0 OP2 A:C26 4.4 26.6 1.0 O A:HOH236 4.4 38.0 1.0 O A:HOH247 4.5 37.0 1.0 C2' A:U8 4.6 27.2 1.0 C8 A:A27 4.7 27.6 1.0 N7 A:G28 4.8 25.3 1.0 C5 A:C26 4.9 26.5 1.0 O A:HOH212 5.0 31.4 1.0

Magnesium binding site 2 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


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 N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:40.9 occ:1.00 O A:HOH210 1.9 37.5 1.0 O A:HOH263 2.3 40.0 1.0 O A:HOH224 2.3 31.9 1.0 O A:HOH258 2.4 43.0 1.0 O A:HOH248 2.4 37.8 1.0 O6 A:G5 4.2 28.7 1.0 N7 A:A4 4.3 27.7 1.0 C2 A:A6 4.4 24.9 1.0 N7 A:G5 4.4 25.1 1.0 N3 A:A6 4.5 25.4 1.0 N6 A:A4 4.6 28.5 1.0

Magnesium binding site 3 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


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 N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:37.8 occ:1.00 O A:HOH201 2.0 36.6 1.0 O A:HOH236 2.0 38.0 1.0 O A:HOH229 2.0 30.4 1.0 OP1 A:G25 3.4 29.1 1.0 OP2 A:G9 4.1 31.1 1.0 P A:G25 4.2 27.5 1.0 OP2 A:G25 4.3 27.3 1.0 O A:HOH240 4.4 32.5 1.0 OP2 A:C26 4.4 26.6 1.0 O A:HOH246 4.5 35.0 1.0 O A:HOH256 4.6 36.1 1.0 OP1 A:G9 4.7 35.6 1.0 O5' A:G25 4.7 26.6 1.0 P A:G9 4.9 31.8 1.0

Magnesium binding site 4 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


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 N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:46.7 occ:1.00 OP1 A:U10 1.9 31.8 1.0 O A:HOH205 2.1 37.8 1.0 O A:HOH232 2.1 43.9 1.0 O A:HOH259 2.2 51.1 1.0 O A:HOH249 2.5 48.6 1.0 O A:HOH254 2.7 52.6 1.0 P A:U10 3.4 35.5 1.0 C3' A:G9 4.0 30.5 1.0 OP2 A:A6 4.1 27.6 1.0 OP2 A:U10 4.2 39.3 1.0 O3' A:G9 4.2 32.2 1.0 O5' A:U10 4.3 32.7 1.0 C5' A:G9 4.3 28.3 1.0 C4' A:G9 4.4 27.8 1.0 C5' A:U10 4.5 30.1 1.0 OP1 A:G9 4.6 35.6 1.0 O A:HOH234 4.6 38.6 1.0 O5' A:G9 4.9 29.7 1.0

Magnesium binding site 5 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


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 N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:33.3 occ:1.00 O A:HOH243 2.0 35.0 1.0 OP1 A:C19 2.1 37.0 1.0 O A:HOH253 2.2 39.3 1.0 P A:C19 3.2 34.3 1.0 OP2 A:C19 3.7 31.0 1.0 O3' A:C18 3.9 36.9 1.0 O A:HOH222 4.2 31.7 1.0 O5' A:C19 4.5 32.9 1.0 OP1 A:C18 4.9 37.6 1.0

Magnesium binding site 6 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


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 N within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:35.6 occ:1.00 O A:HOH241 2.0 34.3 1.0 O B:HOH257 2.0 34.9 1.0 OP2 B:C30 2.0 29.5 1.0 OP2 B:A31 2.1 33.3 1.0 O B:HOH263 2.1 34.5 1.0 P B:C30 3.4 27.4 1.0 P B:A31 3.6 31.4 1.0 O A:HOH226 3.8 39.4 1.0 O B:HOH204 3.9 31.3 1.0 O5' B:C30 4.0 27.6 1.0 C5' B:C30 4.2 26.5 1.0 N7 B:A31 4.3 27.0 1.0 O3' B:C30 4.4 28.2 1.0 OP1 B:C30 4.4 26.8 1.0 OP1 B:A31 4.4 34.8 1.0 O3' B:A29 4.4 25.4 1.0 O5' B:A31 4.4 31.2 1.0 O2' A:A11 4.5 31.1 1.0 C8 B:A31 4.6 27.5 1.0 C3' B:C30 4.7 27.4 1.0 O3' A:A11 5.0 39.4 1.0

Magnesium binding site 7 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


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 N within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:29.3 occ:1.00 O B:HOH265 1.9 27.9 1.0 O B:HOH272 1.9 33.7 1.0 O B:HOH281 2.1 27.0 1.0 O B:HOH230 2.2 25.5 1.0 O B:HOH227 2.2 29.6 1.0 O B:HOH284 2.3 26.5 1.0 O B:HOH242 3.8 30.0 1.0 O B:HOH237 4.0 29.4 1.0 N7 B:A27 4.1 23.1 1.0 O B:HOH282 4.1 27.4 1.0 OP2 B:A27 4.1 26.6 1.0 O6 B:G28 4.2 23.4 1.0 O B:HOH246 4.2 25.3 1.0 O2' B:U8 4.4 22.4 1.0 O B:HOH268 4.5 33.3 1.0 OP2 B:C26 4.6 22.8 1.0 C8 B:A27 4.6 24.8 1.0 N7 B:G28 4.7 23.4 1.0 C2' B:U8 4.8 18.9 1.0 O B:HOH264 4.8 35.4 1.0 C5 B:C26 4.9 23.6 1.0

Magnesium binding site 8 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of A New Fluorescent Rna Aptamer Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:21.8 occ:1.00 O B:HOH234 2.0 23.8 1.0 O B:HOH240 2.1 24.6 1.0 O B:HOH233 2.1 23.0 1.0 O B:HOH282 2.1 27.4 1.0 O B:HOH278 2.2 27.6 1.0 OP1 B:G25 4.1 28.0 1.0 O B:HOH246 4.2 25.3 1.0 O B:HOH284 4.2 26.5 1.0 OP2 B:G9 4.3 25.9 1.0 O B:HOH256 4.4 34.2 1.0 OP2 B:C26 4.4 22.8 1.0 O B:HOH268 4.5 33.3 1.0 OP2 B:G25 4.7 27.9 1.0 P B:G25 4.8 24.9 1.0

Magnesium binding site 9 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of A New Fluorescent Rna Aptamer Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:44.6 occ:1.00 OP1 B:G24 2.4 31.6 1.0 P B:G24 3.5 31.3 1.0 OP2 B:G24 3.8 31.5 1.0 O B:HOH247 4.0 37.2 1.0 O5' B:G24 4.3 29.9 1.0 O B:HOH206 4.4 43.7 1.0 C5' B:G24 4.6 26.3 1.0 O3' B:A23 4.8 31.7 1.0

Magnesium binding site 10 out of 11 in the A New Fluorescent Rna Aptamer Bound with N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of A New Fluorescent Rna Aptamer Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:45.7 occ:1.00 O B:HOH285 2.5 45.4 1.0 O B:HOH273 2.5 43.6 1.0 O B:HOH286 2.7 51.2 1.0 O B:HOH206 2.7 43.7 1.0 OP2 B:A23 2.9 33.9 1.0 N7 B:G24 3.0 29.2 1.0 O B:HOH247 3.7 37.2 1.0 O B:HOH209 3.7 33.1 1.0 C8 B:G24 3.8 28.6 1.0 P B:A23 3.8 34.3 1.0 OP2 B:G24 3.8 31.5 1.0 OP1 B:A23 4.1 35.2 1.0 C5 B:G24 4.1 27.5 1.0 O5' B:A23 4.1 29.9 1.0 O6 B:G24 4.2 28.7 1.0 N2 B:G20 4.3 27.1 1.0 C6 B:G24 4.5 26.5 1.0 N1 B:G20 4.9 27.7 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