Magnesium in PDB 8hzm: A New Fluorescent Rna Aptamer Bound with N, Manganese Soak

The structure of A New Fluorescent Rna Aptamer Bound with N, Manganese Soak, PDB code: 8hzm 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)	39.14 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.694, 46.871, 56.722, 90, 113.7, 90
R / Rfree (%)	20.5 / 25.7

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

Manganese	(Mn)	11 atoms
Potassium	(K)	2 atoms

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

Magnesium binding site 1 out of 5 in the A New Fluorescent Rna Aptamer Bound with N, Manganese Soak


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, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:55.8 occ:1.00 O3' A:C36 1.7 56.8 1.0 O2' A:C36 2.0 67.0 1.0 C3' A:C36 2.7 61.9 1.0 C2' A:C36 2.8 65.5 1.0 C1' A:C36 3.6 57.8 1.0 C4' A:C36 3.9 64.8 1.0 O4' A:C36 4.4 58.0 1.0 N1 A:C36 4.7 55.5 1.0 O2 A:C36 4.8 59.5 1.0

Magnesium binding site 2 out of 5 in the A New Fluorescent Rna Aptamer Bound with N, Manganese Soak


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, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:52.0 occ:1.00 OP2 A:A31 2.2 63.7 1.0 O A:HOH203 2.6 65.4 1.0 OP2 A:C30 2.6 67.0 1.0 P A:A31 3.5 72.6 1.0 O5' A:A31 3.9 65.5 1.0 N7 A:A31 3.9 61.8 1.0 P A:C30 4.0 72.5 1.0 C8 A:A31 4.0 63.3 1.0 O5' A:C30 4.4 64.0 1.0 OP1 A:A31 4.5 74.9 1.0 O3' A:A29 4.5 65.1 1.0 O3' A:C30 4.6 60.3 1.0 C5' A:C30 4.6 65.6 1.0 C3' A:C30 4.7 62.9 1.0

Magnesium binding site 3 out of 5 in the A New Fluorescent Rna Aptamer Bound with N, Manganese Soak


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, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg107 b:63.5 occ:1.00 OP1 A:G25 2.9 47.2 1.0 C2 B:A23 3.0 64.2 1.0 N1 B:A23 3.1 57.5 1.0 P A:G25 4.1 49.0 1.0 N3 B:A23 4.2 61.8 1.0 N1 B:A22 4.3 66.6 1.0 O5' A:G25 4.4 43.5 1.0 OP1 A:G9 4.5 49.8 1.0 OP2 A:C26 4.5 54.2 1.0 C6 B:A23 4.5 55.1 1.0 OP2 A:G25 4.6 41.1 1.0 C5' A:G25 4.8 45.6 1.0 C2 B:A22 4.8 65.2 1.0 OP2 A:G9 4.8 51.2 1.0

Magnesium binding site 4 out of 5 in the A New Fluorescent Rna Aptamer Bound with N, Manganese Soak


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, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg108 b:42.5 occ:1.00 O B:HOH209 1.8 44.0 1.0 OP1 B:A12 2.0 53.6 1.0 P B:A12 3.5 51.5 1.0 O5' B:A12 3.9 49.6 1.0 C5' B:A12 4.0 49.5 1.0 O3' B:A11 4.4 48.9 1.0 OP2 B:A12 4.5 48.2 1.0 O4 B:U10 4.5 44.3 1.0

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


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, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg109 b:61.1 occ:1.00 N7 B:GTP101 2.2 58.3 1.0 C5 B:GTP101 3.1 55.7 1.0 C8 B:GTP101 3.1 59.8 1.0 O6 B:GTP101 3.2 56.3 1.0 O3A B:GTP101 3.3 93.2 1.0 C6 B:GTP101 3.6 52.9 1.0 O1B B:GTP101 4.0 93.2 1.0 O1A B:GTP101 4.1 79.5 1.0 O B:HOH205 4.2 56.9 1.0 N9 B:GTP101 4.3 57.6 1.0 C4 B:GTP101 4.3 55.9 1.0 PA B:GTP101 4.3 87.3 1.0 PB B:GTP101 4.4 103.5 1.0 N7 B:G2 4.5 57.2 1.0 N1 B:GTP101 4.9 53.1 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