Magnesium in PDB 5y85: Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme

The structure of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme, PDB code: 5y85 was solved by L.Zheng, R.L.Micura, A.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.85 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.182, 109.304, 41.739, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 23.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Magnesium atom in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme (pdb code 5y85). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 26 binding sites of Magnesium where determined in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme, PDB code: 5y85:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:37.7 occ:1.00 O A:HOH211 2.1 48.0 1.0 O B:HOH229 2.1 43.9 1.0 O A:HOH201 2.2 64.1 1.0 O A:HOH214 2.2 59.2 1.0 OP2 A:G9 2.3 47.3 1.0 OP2 A:A8 2.3 55.9 1.0 P A:A8 3.6 46.2 1.0 P A:G9 3.7 45.8 1.0 O5' A:A8 3.8 44.4 1.0 O A:HOH210 4.1 59.3 1.0 O4 B:U18 4.2 49.5 1.0 O5' A:G9 4.3 43.9 1.0 N7 A:G9 4.4 44.0 1.0 C3' A:A8 4.5 30.4 1.0 OP1 A:A8 4.6 51.6 1.0 O3' A:A8 4.6 40.1 1.0 C8 A:G9 4.6 43.8 1.0 OP1 A:G9 4.7 50.0 1.0 O3' A:A7 4.7 51.9 1.0 C3' A:A7 4.7 54.6 1.0 O6 B:G17 4.8 45.3 1.0 O B:HOH224 4.8 55.0 1.0 C5' A:A8 4.8 47.2 1.0

Magnesium binding site 2 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:54.7 occ:1.00 O A:HOH215 2.1 78.7 1.0 O A:HOH213 2.1 58.3 1.0 O A:HOH205 2.1 60.4 1.0 O6 A:G16 4.4 53.8 1.0 O6 A:G17 4.4 64.2 1.0 O6 B:G1 4.7 72.3 1.0 N7 A:G16 4.9 51.9 1.0 N4 A:C15 4.9 45.4 1.0

Magnesium binding site 3 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:30.7 occ:1.00 O B:HOH230 2.1 47.7 1.0 OP2 B:C42 2.1 37.9 1.0 O B:HOH216 2.2 50.0 1.0 OP2 B:U43 2.2 41.1 1.0 P B:U43 3.5 45.2 1.0 P B:C42 3.5 50.2 1.0 OP1 B:U43 4.0 45.9 1.0 OP2 B:A45 4.1 63.4 1.0 O3' B:C42 4.2 40.3 1.0 OP1 B:C42 4.2 50.0 1.0 O5' B:C42 4.3 45.8 1.0 O A:HOH209 4.3 62.6 1.0 C5' B:C42 4.5 54.5 1.0 O3' B:G41 4.6 51.9 1.0 C3' B:C42 4.7 43.4 1.0 O5' B:U43 4.7 47.9 1.0 O6 A:G5 4.9 51.7 1.0

Magnesium binding site 4 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:30.3 occ:1.00 O B:HOH234 2.1 55.0 1.0 OP1 B:U43 2.1 45.9 1.0 O B:HOH220 2.1 56.2 1.0 OP2 B:DC44 2.4 53.3 1.0 P B:U43 3.6 45.2 1.0 P B:DC44 3.9 56.5 1.0 C5' B:U43 4.1 45.5 1.0 O5' B:U43 4.1 47.9 1.0 C5' B:DC44 4.1 35.6 1.0 O B:HOH230 4.5 47.7 1.0 O3' B:C42 4.5 40.3 1.0 O5' B:DC44 4.5 57.4 1.0 OP2 B:U43 4.6 41.1 1.0 OP1 B:DC44 4.6 49.4 1.0 O3' B:U43 4.9 55.0 1.0

Magnesium binding site 5 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:37.5 occ:1.00 O B:HOH208 2.1 51.0 1.0 O B:HOH231 2.1 53.1 1.0 O B:HOH246 2.1 67.8 1.0 O B:HOH204 2.2 49.2 1.0 O B:HOH219 2.2 49.6 1.0 O6 B:G41 2.2 47.6 1.0 C6 B:G41 3.4 43.8 1.0 C5 B:G41 4.2 43.8 1.0 N7 B:G41 4.3 37.9 1.0 C5 B:C40 4.3 45.6 1.0 O2 B:U18 4.3 47.1 1.0 O A:HOH204 4.3 50.9 1.0 N1 B:G41 4.5 38.3 1.0 OP1 A:C6 4.5 62.4 1.0 OP2 B:C40 4.6 43.4 1.0 OP2 B:G39 4.6 57.8 1.0 N4 B:C40 4.7 43.2 1.0 O A:HOH202 4.7 57.9 1.0

Magnesium binding site 6 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:32.6 occ:1.00 O B:HOH224 2.1 55.0 1.0 O A:HOH207 2.1 53.6 1.0 O B:HOH243 2.1 75.1 1.0 O D:HOH271 2.1 69.2 1.0 O A:HOH203 2.1 59.6 1.0 O A:HOH210 2.2 59.3 1.0 OP1 A:A8 4.1 51.6 1.0 OP1 B:G17 4.1 71.5 1.0 O A:HOH201 4.1 64.1 1.0 N7 B:G17 4.2 47.8 1.0 C8 B:G17 4.5 62.0 1.0

Magnesium binding site 7 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:37.0 occ:1.00 OP1 B:G38 2.1 56.5 1.0 O B:HOH225 2.1 42.4 1.0 O B:HOH240 2.1 56.7 1.0 O B:HOH226 2.2 57.0 1.0 O B:HOH237 2.2 52.9 1.0 OP1 B:G7 2.3 46.0 1.0 P B:G38 3.4 55.5 1.0 P B:G7 3.5 49.8 1.0 O3' B:G37 3.9 63.9 1.0 O3' B:C6 4.0 55.9 1.0 OP2 B:G38 4.1 53.0 1.0 C3' B:G37 4.2 49.0 1.0 OP2 B:G7 4.2 60.0 1.0 O2' B:C6 4.3 54.1 1.0 C2' B:G37 4.3 46.0 1.0 C8 B:G7 4.4 50.2 1.0 C3' B:C6 4.4 42.0 1.0 O2' B:G17 4.5 53.9 1.0 N7 B:G7 4.5 69.1 1.0 O5' B:G38 4.6 52.8 1.0 O5' B:G7 4.8 48.4 1.0 C5' B:U18 4.9 50.0 1.0 C5' B:G7 4.9 52.4 1.0 C2' B:C6 4.9 36.8 1.0

Magnesium binding site 8 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:57.3 occ:1.00 O B:HOH239 1.7 79.3 1.0 O B:HOH257 1.7 0.9 1.0 O B:HOH211 2.1 83.2 1.0 O B:HOH249 2.3 91.8 1.0 O B:HOH242 2.4 95.6 1.0 O6 B:G49 4.0 85.0 1.0 O B:HOH245 4.4 88.1 1.0 N7 B:G49 4.6 67.0 1.0 C6 B:G49 4.9 63.3 1.0 O4 B:U50 4.9 68.1 1.0

Magnesium binding site 9 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg107 b:94.4 occ:1.00 O B:HOH205 2.0 74.6 1.0 O B:HOH236 2.1 99.7 1.0 O B:HOH256 2.1 0.6 1.0 O B:HOH214 2.2 77.4 1.0 O B:HOH254 2.2 86.9 1.0 O B:HOH245 2.3 88.1 1.0 N7 B:G47 3.6 65.7 1.0 OP2 B:U46 4.1 54.6 1.0 C8 B:G47 4.3 52.0 1.0 O B:HOH242 4.4 95.6 1.0 C5 B:G47 4.7 56.6 1.0 O6 B:G47 4.9 58.2 1.0

Magnesium binding site 10 out of 26 in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg108 b:41.7 occ:1.00 O B:HOH252 2.1 65.2 1.0 O B:HOH241 2.1 54.1 1.0 O B:HOH244 2.1 57.8 1.0 O B:HOH209 2.1 63.0 1.0 O B:HOH233 2.2 59.4 1.0 O B:HOH213 2.2 53.0 1.0 OP2 B:G17 4.0 74.1 1.0 C5' B:G17 4.4 58.0 1.0 O B:HOH227 4.5 47.5 1.0 O6 B:G11 4.5 48.1 1.0 OP2 B:U18 4.6 55.2 1.0 O6 B:G10 4.7 51.9 1.0 N7 B:G10 4.8 75.5 1.0

L.Zheng, E.Mairhofer, M.Teplova, Y.Zhang, J.Ma, D.J.Patel, R.Micura, A.Ren. Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme Nat Commun V. 8 1180 2017.
ISSN: ESSN 2041-1723
PubMed: 29081514
DOI: 10.1038/S41467-017-01276-Y