Magnesium in PDB 3egz: Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch

The structure of Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch, PDB code: 3egz was solved by H.Xiao, T.E.Edwards, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.31 / 2.20
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.835, 120.835, 55.279, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26

The structure of Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch (pdb code 3egz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch, PDB code: 3egz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


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 An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:77.1 occ:0.25 O A:HOH327 3.2 48.7 0.2 CE1 A:PHE270 4.4 49.1 1.0 CG A:PRO271 4.6 33.9 1.0 CZ A:PHE270 4.8 48.5 1.0 CD A:PRO271 5.0 33.2 1.0

Magnesium binding site 2 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


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 An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:47.8 occ:1.00 O B:HOH302 2.0 43.8 1.0 O B:HOH305 2.1 38.3 1.0 O B:HOH301 2.1 34.0 1.0 O B:HOH304 2.2 40.3 1.0 O B:HOH306 2.2 34.0 1.0 O B:HOH303 2.2 42.0 1.0 OP1 B:G9 3.9 36.2 1.0 OP2 B:A22 4.1 46.5 1.0 N7 B:G10 4.2 33.3 1.0 OP1 B:A22 4.2 48.7 1.0 O6 B:G10 4.4 40.5 1.0 O4 B:U11 4.4 47.3 1.0 O B:HOH359 4.4 44.0 1.0 O3' B:A8 4.4 41.3 1.0 O B:HOH407 4.4 35.2 1.0 O2' B:A8 4.6 35.0 1.0 OP2 B:G10 4.6 41.7 1.0 P B:A22 4.6 47.2 1.0 C4' B:A8 4.8 41.3 1.0 P B:G9 4.9 41.1 1.0 C5 B:G10 4.9 35.9 1.0 C6 B:G10 5.0 37.8 1.0 O B:HOH380 5.0 47.8 1.0

Magnesium binding site 3 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


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 An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:54.8 occ:1.00 O B:HOH320 2.0 45.5 1.0 O B:HOH321 2.1 56.7 1.0 O B:HOH312 2.2 36.0 1.0 OP1 B:A8 2.2 47.9 1.0 O B:HOH322 2.3 51.1 1.0 P B:A8 3.5 45.4 1.0 O B:HOH313 3.6 43.0 1.0 OP2 B:A53 3.8 41.2 1.0 O3' B:G7 4.0 45.6 1.0 OP2 B:G9 4.1 40.0 1.0 OP2 B:A8 4.2 41.2 1.0 O5' B:A8 4.6 43.2 1.0 OP1 B:A53 4.6 44.7 1.0 P B:A53 4.7 43.5 1.0 C5' B:A8 5.0 41.2 1.0

Magnesium binding site 4 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


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 An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:71.4 occ:1.00 O B:HOH443 1.8 60.5 1.0 O B:HOH429 2.0 58.6 1.0 OP2 B:G15 2.1 60.8 1.0 O B:HOH430 2.1 70.0 1.0 P B:G15 3.3 64.9 1.0 O5' B:G15 3.7 63.2 1.0 OP1 B:G15 4.1 69.2 1.0 N7 B:G15 4.3 53.0 1.0 C8 B:G15 4.4 54.5 1.0 N7 B:A16 4.5 54.0 1.0 OP1 B:A14 4.5 70.4 1.0 OP2 B:A16 4.6 66.0 1.0 OP2 B:A14 4.6 66.8 1.0 O3' B:A14 4.6 63.4 1.0 N6 B:A16 4.6 55.2 1.0 O5' B:A14 4.7 64.4 1.0 P B:A14 4.8 66.8 1.0 C3' B:A14 4.8 61.2 1.0 O B:HOH448 4.9 62.5 1.0

Magnesium binding site 5 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


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 An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:72.7 occ:1.00 OP2 B:A13 1.9 57.0 1.0 O B:HOH409 2.3 56.0 1.0 P B:A13 3.3 58.9 1.0 O5' B:A13 3.8 58.2 1.0 O6 B:G15 4.0 49.6 1.0 C8 B:A13 4.2 50.0 1.0 N7 B:A13 4.2 50.0 1.0 N7 B:A14 4.2 51.6 1.0 OP1 B:A13 4.3 58.1 1.0 O3' B:G12 4.4 57.2 1.0 C3' B:G12 4.5 55.3 1.0 N6 B:A14 4.8 46.1 1.0 OP2 B:A14 4.8 66.8 1.0 C6 B:G15 4.9 50.5 1.0

Magnesium binding site 6 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:64.3 occ:0.50 OP1 B:U11 2.5 48.7 1.0 O B:HOH334 3.0 58.6 1.0 P B:U11 3.7 43.5 1.0 OP2 B:U11 4.3 43.6 1.0 O3' B:G10 4.4 45.9 1.0 O5' B:U11 4.9 44.8 1.0

Magnesium binding site 7 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:54.0 occ:1.00 O B:HOH427 2.1 50.1 1.0 OP2 B:A55 2.3 43.5 1.0 O B:HOH313 2.3 43.0 1.0 O B:HOH323 2.3 42.8 1.0 OP1 B:A54 2.4 42.1 1.0 P B:A54 3.6 41.8 1.0 P B:A55 3.7 45.6 1.0 OP2 B:A54 4.0 41.1 1.0 OP2 B:G9 4.1 40.0 1.0 O5' B:A54 4.1 38.2 1.0 O B:HOH402 4.2 47.3 1.0 OP2 B:A8 4.3 41.2 1.0 N7 B:A55 4.4 37.2 1.0 OP1 B:A53 4.5 44.7 1.0 C8 B:A8 4.5 38.7 1.0 OP1 B:A55 4.5 47.4 1.0 OP1 B:A8 4.6 47.9 1.0 O5' B:A55 4.6 46.5 1.0 C8 B:A55 4.6 38.8 1.0 O3' B:A54 4.7 43.2 1.0 P B:A8 4.8 45.4 1.0 C3' B:A54 4.8 43.4 1.0 N7 B:A8 4.8 38.9 1.0 O5' B:A8 4.9 43.2 1.0 O3' B:A53 4.9 41.3 1.0 C5' B:A54 5.0 41.8 1.0

Magnesium binding site 8 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg507 b:62.6 occ:1.00 O B:HOH315 2.1 44.5 1.0 O B:HOH335 2.2 52.7 1.0 O B:HOH314 2.3 43.9 1.0 OP2 B:C57 2.3 62.7 1.0 P B:C57 3.7 61.9 1.0 O B:HOH403 4.0 54.3 1.0 O6 B:G21 4.1 41.2 1.0 O6 B:G7 4.3 39.7 1.0 OP1 B:C57 4.3 62.9 1.0 OP1 B:A56 4.3 59.7 1.0 O5' B:A56 4.3 55.1 1.0 OP2 B:A56 4.4 56.1 1.0 N6 B:A6 4.4 45.3 1.0 N7 B:G7 4.5 37.4 1.0 P B:A56 4.5 57.5 1.0 N7 B:A6 4.5 47.3 1.0 O3' B:A56 4.6 60.4 1.0 N1 B:G21 4.7 41.3 1.0 O5' B:C57 4.7 60.5 1.0 C6 B:G21 4.8 39.9 1.0 C3' B:A56 4.9 56.7 1.0 C5 B:A6 5.0 46.4 1.0 C5 B:C57 5.0 48.1 1.0 C6 B:A6 5.0 44.2 1.0

Magnesium binding site 9 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg508 b:60.7 occ:1.00 O B:HOH338 2.1 52.7 1.0 O B:HOH349 2.3 38.8 1.0 O B:HOH337 2.3 46.4 1.0 N7 B:G47 4.0 37.2 1.0 O6 B:G47 4.1 35.5 1.0 O4 B:U48 4.1 36.5 1.0 O4 B:U32 4.4 37.2 1.0 C6 B:G47 4.8 35.0 1.0 C5 B:G47 4.8 37.9 1.0 N6 B:A49 4.8 40.4 1.0 N6 B:A33 4.9 32.7 1.0

Magnesium binding site 10 out of 12 in the Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of An in Vitro Evolved Tetracycline Aptamer and Artificial Riboswitch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg509 b:63.7 occ:1.00 O4 B:U37 2.7 37.8 1.0 O B:HOH340 2.9 37.9 1.0 C4 B:U37 3.6 36.2 1.0 C5 B:U37 3.8 37.7 1.0 N7 B:A36 4.5 34.7 1.0 N3 B:U37 4.9 38.8 1.0 O B:HOH415 5.0 50.1 1.0 N6 B:A36 5.0 36.5 1.0

H.Xiao, T.E.Edwards, A.R.Ferre-D'amare. Structural Basis For Specific, High-Affinity Tetracycline Binding By An in Vitro Evolved Aptamer and Artificial Riboswitch Chem.Biol. V. 15 1125 2008.
ISSN: ISSN 1074-5521
PubMed: 18940672
DOI: 10.1016/J.CHEMBIOL.2008.09.004