Manganese 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:

Potassium	(K)	2 atoms
Magnesium	(Mg)	5 atoms

Pages:

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

Binding sites:

The binding sites of Manganese 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 Manganese atom.
In total 11 binding sites of Manganese where determined in the A New Fluorescent Rna Aptamer Bound with N, Manganese Soak, PDB code: 8hzm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn102 b:55.5 occ:1.00 O A:HOH215 2.2 49.7 1.0 O B:HOH212 2.2 42.9 1.0 O B:HOH210 2.3 43.5 1.0 OP1 B:G25 4.0 45.3 1.0 OP2 B:C26 4.3 39.1 1.0 C2 A:A23 4.4 45.6 1.0 N1 A:A22 4.4 53.3 1.0 N1 A:A23 4.5 46.9 1.0 N6 A:A22 4.8 46.1 1.0 P B:G25 4.8 45.0 1.0 OP2 B:G25 4.8 54.1 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn103 b:74.8 occ:1.00 N7 A:G24 2.4 43.1 1.0 O A:HOH201 2.4 48.5 1.0 C8 A:G24 3.3 44.0 1.0 C5 A:G24 3.4 37.3 1.0 O6 A:G24 3.6 43.0 1.0 OP2 A:G24 3.6 49.0 1.0 C6 A:G24 3.9 40.1 1.0 OP2 A:A23 4.4 40.8 1.0 N9 A:G24 4.5 44.1 1.0 C4 A:G24 4.5 42.5 1.0 N7 A:G25 4.7 45.8 1.0 O6 A:G25 5.0 44.5 1.0 N2 A:G20 5.0 42.0 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 A:Mn104 b:70.0 occ:1.00 OP1 A:C18 2.3 61.3 1.0 P A:C18 3.7 57.4 1.0 O5' A:C18 4.2 54.2 1.0 OP2 A:C18 4.4 54.8 1.0 C5' A:C18 4.5 47.8 1.0 O3' A:G17 4.8 59.5 1.0 OP2 A:C19 4.8 51.5 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 A:Mn105 b:52.8 occ:1.00 OP2 A:G20 2.0 49.9 1.0 O A:HOH214 2.3 43.0 1.0 P A:G20 3.4 41.6 1.0 O5' A:G20 3.7 47.4 1.0 OP1 A:G20 4.3 44.7 1.0 OP2 A:A21 4.3 41.9 1.0 C8 A:G20 4.4 43.4 1.0 N7 A:G20 4.4 38.6 1.0 O3' A:C19 4.5 42.4 1.0 OP2 A:C19 4.6 51.5 1.0 O5' A:C19 4.6 56.8 1.0 C3' A:C19 4.7 46.0 1.0 P A:C19 5.0 54.0 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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 A:Mn106 b:83.6 occ:1.00 OP2 A:A27 2.7 64.8 1.0 OP2 A:U8 4.0 71.5 1.0 P A:A27 4.0 58.2 1.0 N7 A:G28 4.1 47.8 1.0 N7 A:A27 4.2 48.2 1.0 C8 A:A27 4.2 47.0 1.0 O5' A:A27 4.2 48.8 1.0 O6 A:G28 4.4 47.1 1.0 OP2 A:C26 4.8 54.2 1.0 C2' A:U8 4.8 43.5 1.0 O2' A:U8 4.8 56.4 1.0 C3' A:C26 4.9 53.9 1.0 O5' A:U8 4.9 60.5 1.0 O3' A:C26 5.0 55.8 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of A New Fluorescent Rna Aptamer Bound with N, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:84.5 occ:1.00 OP1 A:U10 2.2 54.3 1.0 P A:U10 3.6 45.6 1.0 OP2 A:A6 3.9 44.3 1.0 C3' A:G9 4.3 43.0 1.0 C5' A:G9 4.4 46.2 1.0 OP2 A:U10 4.4 49.0 1.0 O3' A:G9 4.5 46.8 1.0 O5' A:U10 4.5 45.9 1.0 C4' A:G9 4.5 45.8 1.0 C5' A:U10 4.6 41.7 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of A New Fluorescent Rna Aptamer Bound with N, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:52.8 occ:1.00 O B:HOH203 1.6 40.4 1.0 OP2 B:A31 2.2 44.0 1.0 OP2 B:C30 2.2 45.4 1.0 O B:HOH215 2.3 40.9 1.0 P B:A31 3.6 48.8 1.0 O B:HOH207 3.7 40.0 1.0 P B:C30 3.7 43.0 1.0 O5' B:C30 4.2 43.5 1.0 OP1 B:A31 4.3 48.8 1.0 C5' B:C30 4.3 44.3 1.0 O5' B:A31 4.5 46.1 1.0 O3' B:C30 4.5 39.5 1.0 N7 B:A31 4.6 48.9 1.0 O3' B:A29 4.6 45.4 1.0 OP1 B:C30 4.6 33.7 1.0 C3' B:C30 4.8 44.6 1.0 C8 B:A31 4.8 45.5 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of A New Fluorescent Rna Aptamer Bound with N, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn103 b:66.2 occ:1.00 O B:HOH218 1.9 48.1 1.0 O B:HOH213 2.4 43.9 1.0 O B:HOH217 2.7 41.8 1.0 O B:HOH211 2.9 47.9 1.0 OP2 B:A27 3.3 48.3 1.0 OP2 B:U8 3.9 58.4 1.0 N7 B:A27 4.4 52.5 1.0 N7 B:G28 4.4 43.5 1.0 C8 B:A27 4.6 47.9 1.0 O5' B:U8 4.6 48.8 1.0 P B:A27 4.6 41.2 1.0 O2' B:U8 4.7 40.7 1.0 C2' B:U8 4.7 42.8 1.0 O5' B:A27 4.8 47.9 1.0 P B:U8 4.9 56.0 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of A New Fluorescent Rna Aptamer Bound with N, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn104 b:70.2 occ:1.00 OP1 B:U10 1.9 49.1 1.0 P B:U10 3.3 41.2 1.0 OP2 B:U10 3.9 55.3 1.0 C3' B:G9 4.0 46.2 1.0 O3' B:G9 4.2 47.6 1.0 OP2 B:A6 4.2 43.9 1.0 C5' B:G9 4.3 32.9 1.0 O5' B:U10 4.4 43.2 1.0 C4' B:G9 4.4 39.9 1.0 O B:HOH208 4.6 40.9 1.0 C5' B:U10 4.6 44.4 1.0 O5' B:G9 4.9 30.6 1.0 OP1 B:G9 4.9 44.8 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of A New Fluorescent Rna Aptamer Bound with N, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn105 b:83.3 occ:1.00 OP2 B:G20 2.3 54.4 1.0 P B:G20 3.5 52.5 1.0 O5' B:G20 3.6 57.5 1.0 N7 B:G20 3.8 44.6 1.0 C8 B:G20 3.9 46.7 1.0 O3' B:C19 4.5 55.7 1.0 OP1 B:G20 4.5 59.5 1.0 C3' B:C19 4.5 53.5 1.0 OP2 B:A21 4.6 60.5 1.0 OP2 B:C19 4.8 55.8 1.0 O5' B:C19 4.9 56.6 1.0 C5 B:G20 4.9 47.3 1.0 C5' B:G20 5.0 56.4 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