Magnesium in PDB 7eog: Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak

The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak, PDB code: 7eog 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)	46.07 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.925, 34.771, 58.552, 90, 128.11, 90
R / Rfree (%)	19.2 / 21.8

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

Iridium

(Ir)

3 atoms

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

Magnesium binding site 1 out of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:16.7 occ:1.00 O A:HOH287 2.1 16.3 1.0 OP2 A:A30 2.1 17.1 1.0 O A:HOH236 2.2 16.9 1.0 O A:HOH248 2.2 15.4 1.0 O A:HOH286 2.2 15.7 1.0 O A:HOH346 2.2 14.1 1.0 P A:A30 3.5 17.2 1.0 O A:HOH367 3.8 14.6 1.0 O5' A:A30 3.8 16.5 1.0 O A:HOH303 4.0 17.9 1.0 O A:HOH223 4.1 16.1 1.0 O4 A:U32 4.1 16.8 1.0 N7 A:A30 4.2 18.0 1.0 O A:HOH227 4.2 20.7 1.0 C8 A:A30 4.3 16.4 1.0 N7 A:A31 4.3 16.5 1.0 O A:HOH239 4.3 15.5 1.0 OP1 A:G37 4.4 19.2 1.0 OP1 A:A30 4.4 14.8 1.0 OP1 A:C29 4.4 18.4 1.0 O3' A:C29 4.5 16.1 1.0 N6 A:A31 4.6 19.3 1.0 OP2 A:A31 4.7 15.4 1.0 C3' A:C29 4.7 17.2 1.0 O5' A:C29 4.9 19.0 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:17.8 occ:1.00 OP2 A:U32 2.1 16.8 1.0 O A:HOH268 2.1 16.0 1.0 O A:HOH278 2.1 16.0 1.0 O A:HOH330 2.1 14.4 1.0 O A:HOH364 2.2 17.9 1.0 O A:HOH235 2.2 15.7 1.0 P A:U32 3.4 16.6 1.0 O A:HOH348 3.6 32.6 1.0 O5' A:U32 3.9 18.1 1.0 O A:HOH340 4.1 16.0 1.0 OP1 A:A31 4.1 15.8 1.0 OP1 A:U32 4.2 18.7 1.0 OP2 A:G34 4.3 16.6 1.0 OP2 A:C33 4.4 18.4 1.0 OP1 A:G34 4.4 17.4 1.0 O A:HOH241 4.4 26.0 1.0 C5 A:U32 4.5 15.6 1.0 OP2 A:A31 4.5 15.4 1.0 O3' A:A31 4.6 17.4 1.0 P A:A31 4.6 15.2 1.0 C6 A:U32 4.7 14.7 1.0 O5' A:A31 4.7 16.5 1.0 P A:G34 4.8 15.6 1.0 C3' A:A31 4.9 15.1 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:20.1 occ:1.00 OP2 A:U42 2.1 21.7 1.0 O A:HOH359 2.1 20.3 1.0 O A:HOH250 2.1 19.0 1.0 O A:HOH279 2.1 16.2 1.0 O A:HOH361 2.2 21.4 1.0 O A:HOH333 2.2 20.5 1.0 P A:U42 3.4 20.4 1.0 O5' A:U42 3.9 20.9 1.0 O A:HOH283 4.0 19.4 1.0 O3' A:G41 4.1 18.6 1.0 O A:HOH253 4.2 21.2 1.0 O2' A:G41 4.2 17.8 1.0 O A:HOH261 4.2 20.5 1.0 O A:HOH285 4.4 21.8 1.0 O6 A:G4 4.4 16.5 1.0 N4 A:C3 4.5 15.5 1.0 O A:HOH377 4.5 27.0 1.0 N4 A:C5 4.6 15.7 1.0 O A:HOH351 4.6 33.1 1.0 OP1 A:U42 4.6 25.0 1.0 N7 A:G4 4.6 17.4 1.0 O A:HOH325 4.7 16.6 1.0 C5 A:C3 4.7 14.1 1.0 C3' A:G41 4.8 19.9 1.0 C4 A:C3 5.0 12.7 1.0 C2' A:G41 5.0 18.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:16.3 occ:1.00 OP2 A:U8 2.0 16.0 1.0 OP2 A:C7 2.1 15.8 1.0 N7 A:G9 2.1 15.1 1.0 O A:HOH327 2.1 16.7 1.0 O A:HOH324 2.1 15.9 1.0 O A:HOH350 2.2 18.3 1.0 C8 A:G9 3.0 14.7 1.0 C5 A:G9 3.2 15.4 1.0 P A:U8 3.4 17.0 1.0 P A:C7 3.5 16.2 1.0 O6 A:G9 3.7 15.8 1.0 O A:HOH374 3.8 22.2 1.0 C6 A:G9 3.8 15.3 1.0 OP1 A:C7 4.1 16.1 1.0 O3' A:C7 4.1 16.5 1.0 C5 A:U8 4.1 15.8 1.0 O A:HOH249 4.1 26.2 1.0 O A:HOH297 4.2 16.8 1.0 N9 A:G9 4.2 14.3 1.0 OP1 A:U8 4.3 16.2 1.0 O5' A:U8 4.3 16.4 1.0 O5' A:C7 4.3 16.6 1.0 C4 A:G9 4.4 15.6 1.0 O3' A:A6 4.4 16.6 1.0 C3' A:C7 4.5 14.9 1.0 C5' A:C7 4.6 17.5 1.0 C6 A:U8 4.6 14.9 1.0 O A:HOH260 4.7 25.6 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:28.0 occ:1.00 O A:HOH311 1.9 21.6 1.0 O A:HOH391 2.1 29.1 1.0 O A:HOH231 2.3 22.7 1.0 O A:HOH218 3.8 23.3 1.0 N4 A:C48 4.0 18.5 1.0 O A:HOH358 4.1 26.0 1.0 O A:HOH292 4.2 22.6 1.0 N7 A:G47 4.3 16.1 1.0 O A:HOH363 4.3 26.0 1.0 O6 A:G47 4.4 17.1 1.0 O A:HOH244 4.4 25.4 1.0 O A:HOH319 4.7 32.2 1.0 C5 A:C46 4.9 19.3 1.0 C5 A:G47 4.9 16.2 1.0 N4 A:C46 4.9 17.8 1.0 C6 A:G47 5.0 16.1 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