Magnesium in PDB 8hzl: A New Fluorescent Rna APTAMER_III Bound with N

The structure of A New Fluorescent Rna APTAMER_III Bound with N, PDB code: 8hzl 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)	26.24 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.62, 53.931, 81.826, 90, 105.87, 90
R / Rfree (%)	18.1 / 24.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Magnesium atom in the A New Fluorescent Rna APTAMER_III Bound with N (pdb code 8hzl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 23 binding sites of Magnesium where determined in the A New Fluorescent Rna APTAMER_III Bound with N, PDB code: 8hzl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:52.0 occ:1.00 OP2 A:A79 2.2 56.1 1.0 OP2 A:C78 2.5 46.2 1.0 P A:A79 3.7 54.8 1.0 N7 A:A79 3.8 40.1 1.0 P A:C78 3.9 47.7 1.0 C8 A:A79 4.1 41.4 1.0 O5' A:A79 4.3 46.5 1.0 O5' A:C78 4.4 36.7 1.0 O3' A:A77 4.6 39.0 1.0 O3' A:C78 4.6 43.7 1.0 OP1 A:A79 4.6 55.1 1.0 C5' A:C78 4.8 39.3 1.0 C3' A:C78 4.9 44.0 1.0

Magnesium binding site 2 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:62.6 occ:1.00 OP2 A:A61 2.1 53.0 1.0 O A:HOH202 2.1 42.4 1.0 O A:HOH207 2.5 52.1 1.0 OP2 A:C60 2.9 52.2 1.0 P A:A61 3.3 61.7 1.0 O5' A:A61 3.9 51.9 1.0 N7 A:A61 3.9 46.6 1.0 OP1 A:A61 4.0 59.6 1.0 C8 A:A61 4.1 46.5 1.0 P A:C60 4.1 62.2 1.0 O5' A:C60 4.3 56.7 1.0 O3' A:C60 4.5 53.8 1.0 O3' A:A59 4.6 49.3 1.0 C5' A:C60 4.8 58.5 1.0 C3' A:C60 4.9 51.1 1.0

Magnesium binding site 3 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:52.1 occ:1.00 O A:HOH232 2.0 39.3 1.0 O A:HOH247 2.1 42.0 1.0 O A:HOH257 2.5 40.0 1.0 O6 A:G76 3.5 36.0 1.0 N7 A:G76 3.6 33.7 1.0 O2' A:U8 3.6 53.2 1.0 C05 A:NI4111 4.2 35.9 1.0 C2' A:U8 4.2 45.2 1.0 C6 A:G76 4.3 31.3 1.0 C5 A:G76 4.3 32.1 1.0 OP2 A:C75 4.4 37.6 1.0 C5 A:C75 4.5 31.7 1.0 C06 A:NI4111 4.6 36.2 1.0 C8 A:G76 4.7 29.8 1.0 C6 A:C75 4.9 31.3 1.0 OP2 A:U8 4.9 57.2 1.0

Magnesium binding site 4 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:48.3 occ:1.00 O A:HOH224 2.2 45.4 1.0 O A:HOH206 2.4 47.3 1.0 N7 A:G9 3.6 48.6 1.0 O6 A:G76 3.8 36.0 1.0 O2 A:C14 3.8 42.7 1.0 N3 A:C14 3.9 52.2 1.0 O2' A:U8 3.9 53.2 1.0 C8 A:G9 3.9 49.1 1.0 C2 A:C14 4.0 46.4 1.0 C5 A:G9 4.5 48.8 1.0 C6 A:G76 4.6 31.3 1.0 N1 A:G76 4.7 28.7 1.0 C4 A:C14 4.7 49.2 1.0 O3' A:U8 4.8 49.0 1.0 O2' A:C14 4.9 46.5 1.0 C06 A:NI4111 4.9 36.2 1.0 N1 A:C14 5.0 44.8 1.0 N9 A:G9 5.0 51.5 1.0

Magnesium binding site 5 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:40.0 occ:1.00 O A:HOH205 1.9 38.1 1.0 O A:HOH208 2.1 37.6 1.0 OP1 A:U25 2.3 30.4 1.0 P A:U25 3.8 37.6 1.0 OP1 A:G24 4.2 37.5 1.0 OP2 A:A21 4.2 29.6 1.0 C5' A:G24 4.3 34.8 1.0 C3' A:G24 4.3 30.5 1.0 O3' A:G24 4.6 34.4 1.0 C4' A:G24 4.6 35.7 1.0 O5' A:U25 4.6 36.9 1.0 OP2 A:U25 4.6 38.7 1.0 C5' A:U25 4.9 33.6 1.0 O5' A:G24 4.9 34.2 1.0

Magnesium binding site 6 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:43.6 occ:1.00 O A:HOH222 2.1 47.2 1.0 O A:HOH241 2.1 30.2 1.0 O A:HOH230 2.3 31.4 1.0 N7 A:G67 2.9 32.1 1.0 O A:HOH229 3.3 32.2 1.0 OP2 A:G67 3.5 38.8 1.0 C8 A:G67 3.8 30.7 1.0 OP2 A:C66 3.8 44.9 1.0 C5 A:G67 4.0 27.9 1.0 O6 A:G67 4.2 30.9 1.0 C05 A:NI4112 4.2 29.8 1.0 O5' A:C66 4.3 40.7 1.0 C6 A:G67 4.5 30.9 1.0 C5 A:C66 4.6 35.4 1.0 C6 A:C66 4.6 33.7 1.0 P A:C66 4.7 42.1 1.0 C04 A:NI4112 4.7 27.3 1.0 P A:G67 4.8 40.9 1.0 OP2 A:U23 4.9 39.5 1.0 C06 A:NI4112 5.0 31.1 1.0

Magnesium binding site 7 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:46.5 occ:1.00 O A:HOH217 2.0 40.6 1.0 O A:HOH251 2.3 45.6 1.0 OP2 A:A30 3.4 43.6 1.0 N4 A:C32 3.4 33.5 1.0 O6 A:G31 3.6 30.9 1.0 O6 A:G65 4.0 36.1 1.0 O A:HOH227 4.1 35.6 1.0 N7 A:G31 4.2 29.6 1.0 N4 A:C64 4.3 38.5 1.0 C6 A:G31 4.4 32.2 1.0 P A:A30 4.6 37.9 1.0 C5 A:G31 4.6 31.5 1.0 C4 A:C32 4.7 31.7 1.0

Magnesium binding site 8 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:55.2 occ:1.00 O A:HOH216 2.2 43.6 1.0 O A:HOH228 2.6 44.5 1.0 OP1 A:U40 3.2 42.1 1.0 OP1 A:G39 4.6 42.4 1.0 P A:U40 4.6 53.2 1.0 OP2 A:A36 4.9 40.5 1.0

Magnesium binding site 9 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:40.5 occ:1.00 O A:HOH239 2.4 31.1 1.0 O A:HOH211 2.6 37.0 1.0 OP2 A:A57 2.6 39.3 1.0 O A:HOH209 2.8 34.9 1.0 N7 A:G58 3.0 37.3 1.0 OP2 A:G58 3.0 35.5 1.0 O5' A:A57 3.1 38.7 1.0 P A:A57 3.4 47.0 1.0 C8 A:A57 3.5 37.4 1.0 C8 A:G58 3.7 36.6 1.0 N7 A:A57 3.8 34.3 1.0 C3' A:A57 4.1 37.1 1.0 C5 A:G58 4.2 35.6 1.0 OP1 A:A57 4.3 49.0 1.0 P A:G58 4.3 45.2 1.0 C5' A:A57 4.3 39.2 1.0 N9 A:A57 4.4 36.3 1.0 C05 A:NI4113 4.4 33.1 1.0 O6 A:G58 4.6 32.6 1.0 C04 A:NI4113 4.7 32.5 1.0 O3' A:A57 4.7 41.2 1.0 C4' A:A57 4.7 34.6 1.0 O3' A:C56 4.7 42.7 1.0 C5 A:A57 4.7 34.5 1.0 O5' A:G58 4.8 38.2 1.0 C6 A:G58 4.8 34.6 1.0 C2' A:A57 4.9 42.2 1.0 O4' A:A57 4.9 42.4 1.0 OP2 A:U38 4.9 36.8 1.0 C3' A:C56 5.0 40.5 1.0 N9 A:G58 5.0 35.8 1.0 C1' A:A57 5.0 38.8 1.0

Magnesium binding site 10 out of 23 in the A New Fluorescent Rna APTAMER_III 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_III Bound with N within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:32.4 occ:1.00 O A:HOH250 2.3 25.6 1.0 O A:HOH210 2.4 22.4 1.0 O A:HOH204 2.4 25.5 1.0 OP2 A:C69 2.5 25.3 1.0 N7 A:A70 2.7 28.5 1.0 OP2 A:A70 2.9 29.5 1.0 C8 A:A70 3.4 33.6 1.0 O A:HOH214 3.5 24.5 1.0 P A:C69 3.6 25.2 1.0 O5' A:C69 3.7 30.4 1.0 C5 A:A70 3.8 30.5 1.0 O3' A:A68 4.0 27.5 1.0 C5' A:C69 4.0 31.2 1.0 N6 A:A70 4.2 28.5 1.0 P A:A70 4.2 34.8 1.0 C3' A:C69 4.4 30.1 1.0 C6 A:A70 4.5 30.0 1.0 O5' A:A70 4.6 32.3 1.0 N9 A:A70 4.7 32.7 1.0 O3' A:C69 4.7 29.2 1.0 C4' A:C69 4.8 31.0 1.0 C4 A:A70 4.9 31.5 1.0 OP1 A:C69 5.0 23.7 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