Manganese in PDB 7eoi: Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak

The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak, PDB code: 7eoi 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)	35.99 / 1.92
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.619, 34.702, 54.141, 90, 122.78, 90
R / Rfree (%)	21.5 / 24.3

The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak (pdb code 7eoi). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak, PDB code: 7eoi:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:37.7 occ:1.00 O A:HOH215 2.1 34.6 1.0 O A:HOH285 2.1 39.9 1.0 O A:HOH259 2.2 32.4 1.0 N7 A:G1 2.3 27.3 1.0 O A:HOH210 2.4 34.0 1.0 O A:HOH233 2.5 34.6 1.0 C5 A:G1 3.2 23.2 1.0 O6 A:G1 3.3 21.5 1.0 C8 A:G1 3.3 24.8 1.0 C6 A:G1 3.6 24.1 1.0 C4 A:G1 4.4 23.6 1.0 O A:HOH267 4.4 31.9 1.0 OP2 A:G1 4.4 33.9 1.0 N9 A:G1 4.4 25.2 1.0 O6 A:G2 4.6 30.8 1.0 N1 A:G1 5.0 24.0 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:39.0 occ:1.00 OP2 A:U42 2.0 35.3 1.0 O A:HOH278 2.2 29.8 1.0 O A:HOH223 2.3 30.6 1.0 O A:HOH249 2.3 29.6 1.0 O A:HOH258 2.4 30.1 1.0 O A:HOH265 2.4 27.6 1.0 P A:U42 3.4 37.1 1.0 O5' A:U42 3.9 37.8 1.0 O3' A:G41 4.1 39.8 1.0 O2' A:G41 4.2 37.6 1.0 O A:HOH209 4.2 28.2 1.0 O A:HOH225 4.2 28.7 1.0 O6 A:G4 4.5 27.6 1.0 OP1 A:U42 4.6 36.2 1.0 N4 A:C5 4.7 23.1 1.0 N7 A:G4 4.7 25.8 1.0 C3' A:G41 4.8 33.4 1.0 N4 A:C3 4.8 21.7 1.0 C5 A:C3 5.0 21.8 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:28.1 occ:1.00 OP2 A:U8 2.0 30.1 1.0 O A:HOH248 2.0 26.7 1.0 OP2 A:C7 2.0 28.9 1.0 O A:HOH257 2.2 26.9 1.0 O A:HOH252 2.2 23.2 1.0 N7 A:G9 2.3 25.1 1.0 C8 A:G9 3.2 26.2 1.0 C5 A:G9 3.4 27.6 1.0 P A:C7 3.4 31.0 1.0 P A:U8 3.5 32.5 1.0 O6 A:G9 3.9 28.0 1.0 C6 A:G9 4.0 25.4 1.0 OP1 A:C7 4.1 26.7 1.0 O3' A:C7 4.1 29.1 1.0 C5 A:U8 4.3 28.1 1.0 OP1 A:U8 4.3 33.0 1.0 O5' A:C7 4.3 28.2 1.0 O A:HOH245 4.4 33.5 1.0 O5' A:U8 4.4 28.4 1.0 N9 A:G9 4.4 27.8 1.0 O3' A:A6 4.4 29.5 1.0 C5' A:C7 4.5 28.6 1.0 C3' A:C7 4.5 26.3 1.0 C4 A:G9 4.6 29.4 1.0 C6 A:U8 4.8 28.3 1.0 O A:HOH224 4.9 32.5 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:27.1 occ:1.00 O A:HOH251 2.1 22.9 1.0 O A:HOH241 2.1 28.1 1.0 OP2 A:A30 2.1 26.3 1.0 O A:HOH263 2.2 25.4 1.0 O A:HOH213 2.2 29.1 1.0 O A:HOH219 2.3 27.5 1.0 P A:A30 3.5 23.7 1.0 O A:HOH271 3.8 21.9 1.0 O5' A:A30 3.8 27.0 1.0 O A:HOH221 4.2 31.0 1.0 O4 A:U32 4.2 28.3 1.0 O A:HOH218 4.2 25.5 1.0 O A:HOH214 4.2 24.3 1.0 N7 A:A30 4.2 24.4 1.0 C8 A:A30 4.3 26.6 1.0 OP1 A:C29 4.3 28.0 1.0 OP1 A:A30 4.4 23.9 1.0 OP1 A:G37 4.4 27.4 1.0 N7 A:A31 4.4 26.1 1.0 O A:HOH230 4.6 18.8 1.0 O3' A:C29 4.6 27.5 1.0 OP2 A:A31 4.7 21.1 1.0 O5' A:C29 4.8 25.4 1.0 C3' A:C29 4.8 27.6 1.0 N6 A:A31 4.9 27.1 1.0 P A:C29 4.9 33.3 1.0 OP2 A:C29 5.0 30.4 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:26.4 occ:1.00 O A:HOH226 2.0 25.5 1.0 O A:HOH240 2.0 22.9 1.0 O A:HOH253 2.0 24.4 1.0 OP2 A:U32 2.1 31.2 1.0 O A:HOH264 2.2 28.5 1.0 O A:HOH268 2.2 24.9 1.0 P A:U32 3.5 33.1 1.0 O5' A:U32 4.0 32.1 1.0 O A:HOH255 4.2 26.6 1.0 OP2 A:G34 4.2 27.0 1.0 OP1 A:U32 4.2 30.4 1.0 OP1 A:A31 4.3 23.9 1.0 OP2 A:C33 4.3 33.0 1.0 OP1 A:G34 4.4 24.1 1.0 C5 A:U32 4.4 22.5 1.0 O3' A:A31 4.6 29.9 1.0 C6 A:U32 4.7 24.6 1.0 OP2 A:A31 4.7 21.1 1.0 P A:A31 4.8 24.8 1.0 P A:G34 4.9 24.6 1.0 C3' A:A31 4.9 26.2 1.0 O5' A:A31 4.9 22.3 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:42.3 occ:1.00 O A:HOH202 2.2 38.6 1.0 O A:HOH256 2.3 28.4 1.0 O A:HOH220 2.3 35.8 1.0 O A:HOH284 2.3 41.2 1.0 O A:HOH244 2.4 35.8 1.0 N7 A:G41 2.5 35.1 1.0 O23 A:J8F101 2.9 42.2 1.0 C8 A:G41 3.3 31.2 1.0 C5 A:G41 3.5 34.5 1.0 O6 A:G41 3.8 30.7 1.0 C6 A:G41 4.0 32.5 1.0 C21 A:J8F101 4.1 38.2 1.0 OP2 A:C5 4.1 21.2 1.0 N6 A:A6 4.3 31.4 1.0 N9 A:G41 4.5 32.7 1.0 N7 A:A6 4.6 27.8 1.0 C4 A:G41 4.7 32.7 1.0 N22 A:J8F101 4.9 36.0 1.0 C20 A:J8F101 5.0 37.4 1.0

K.Huang, X.Chen, C.Li, Q.Song, H.Li, L.Zhu, Y.Yang, A.Ren. Structure-Based Investigation of Fluorogenic Pepper Aptamer. Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
PubMed: 34725509
DOI: 10.1038/S41589-021-00884-6