Magnesium in PDB 4oji: Crystal Structure of Twister Ribozyme

The structure of Crystal Structure of Twister Ribozyme, PDB code: 4oji was solved by Y.Liu, T.J.Wilson, S.A.Mcphee, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.96 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.380, 55.380, 175.471, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Twister Ribozyme (pdb code 4oji). 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 Twister Ribozyme, PDB code: 4oji:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Twister Ribozyme


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 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:33.1 occ:1.00 O A:HOH245 1.9 21.3 1.0 O A:HOH246 2.0 28.1 1.0 O A:HOH249 2.0 39.0 1.0 O A:HOH248 2.0 30.7 1.0 O A:HOH250 2.2 22.7 1.0 O A:HOH247 2.2 27.6 1.0 O6 A:G23 4.0 24.2 1.0 O A:HOH220 4.1 45.1 1.0 O A:HOH216 4.2 30.6 1.0 O A:HOH214 4.2 30.0 1.0 OP2 A:A29 4.2 32.3 1.0 N7 A:G23 4.2 23.6 1.0 N7 A:G22 4.3 23.2 1.0 O4 A:U24 4.3 16.8 1.0 O6 A:G22 4.4 27.4 1.0 O2' A:A29 4.7 32.6 1.0 C2' A:A29 4.8 35.1 1.0 C6 A:G23 4.8 18.6 1.0 C5 A:G22 4.9 16.1 1.0 C6 A:G22 4.9 21.5 1.0 C5 A:G23 4.9 16.0 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Twister Ribozyme


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 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:62.0 occ:1.00 O A:HOH225 2.0 48.7 1.0 O A:HOH228 2.1 48.7 1.0 O A:HOH223 2.2 31.2 1.0 O A:HOH226 2.3 42.1 1.0 O A:HOH224 2.4 36.5 1.0 O A:HOH227 2.5 49.2 1.0 O A:HOH201 3.9 32.5 1.0 N7 A:A41 4.3 34.3 1.0 O A:HOH203 4.6 27.7 1.0 OP2 A:A8 4.6 30.4 1.0 N6 A:A41 4.6 28.1 1.0 O6 A:G42 4.7 27.8 1.0 N6 A:A10 4.8 22.9 1.0 OP1 A:A8 4.9 28.8 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Twister Ribozyme


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 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:77.1 occ:1.00 O A:HOH230 2.2 65.3 1.0 O A:HOH229 2.3 46.1 1.0 O A:HOH244 2.7 44.3 1.0 O A:HOH222 2.8 45.7 1.0 O A:HOH231 4.6 44.7 1.0 OP2 A:G49 4.7 49.2 1.0 N7 A:G50 4.9 28.0 1.0 OP2 A:G50 4.9 36.2 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Twister Ribozyme


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 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:34.2 occ:1.00 O A:HOH207 2.0 32.7 1.0 O A:HOH208 2.0 44.0 1.0 OP1 A:C26 2.0 26.6 1.0 OP2 A:U24 2.1 26.3 1.0 O A:HOH205 2.2 26.5 1.0 O A:HOH206 2.3 30.8 1.0 P A:C26 3.2 25.7 1.0 O3' A:C25 3.3 41.9 1.0 P A:U24 3.6 23.7 1.0 C5' A:C26 3.8 36.0 1.0 O5' A:C26 4.0 39.7 1.0 OP1 A:U24 4.3 38.1 1.0 O5' A:U24 4.4 29.5 1.0 OP2 A:C26 4.4 32.8 1.0 O A:HOH214 4.4 30.0 1.0 O3' A:G23 4.5 24.2 1.0 O5' A:G23 4.5 37.9 1.0 OP1 A:G23 4.6 37.2 1.0 C3' A:G23 4.6 19.7 1.0 C3' A:C25 4.7 29.3 1.0 C5 A:U24 4.7 14.2 1.0 OP2 A:G23 4.7 32.2 1.0 P A:G23 4.8 36.8 1.0 O2' A:C25 4.9 41.0 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Twister Ribozyme


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 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:27.9 occ:1.00 O A:HOH209 2.0 32.4 1.0 O A:HOH212 2.0 30.9 1.0 O A:HOH213 2.0 28.5 1.0 O A:HOH210 2.0 31.4 1.0 OP1 A:DU6 2.1 26.6 1.0 O A:HOH211 2.2 23.0 1.0 P A:DU6 3.5 26.4 1.0 O A:HOH232 4.0 35.0 1.0 OP2 A:DU6 4.2 39.6 1.0 N6 A:A46 4.3 26.6 1.0 O5' A:DU6 4.3 36.7 1.0 C5' A:DU6 4.3 27.8 1.0 O A:HOH236 4.3 40.0 1.0 O6 A:G47 4.4 27.4 1.0 O A:HOH218 4.4 40.1 1.0 O A:HOH235 4.5 51.8 1.0 O3' A:C5 4.5 40.2 1.0 C3' A:C5 4.5 24.5 1.0 OP2 A:C5 4.6 36.9 1.0 O5' A:C5 4.6 28.1 1.0 N7 A:G47 4.7 28.5 1.0 O A:HOH239 4.8 48.7 1.0

Y.Liu, T.J.Wilson, S.A.Mcphee, D.M.Lilley. Crystal Structure and Mechanistic Investigation of the Twister Ribozyme. Nat.Chem.Biol. V. 10 739 2014.
ISSN: ISSN 1552-4450
PubMed: 25038788
DOI: 10.1038/NCHEMBIO.1587