Manganese in PDB 5y87: 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: 5y87 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)	42.07 / 2.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.221, 108.963, 41.794, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Manganese atom in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme (pdb code 5y87). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 22 binding sites of Manganese where determined in the Structure-Based Insights Into Self-Cleavage By A Four-Way Junctional Twister-Sister Ribozyme, PDB code: 5y87:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 22 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 Manganese with other atoms in the Mn 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:Mn101 b:41.3 occ:1.00 O A:HOH201 2.3 27.8 1.0 O B:HOH224 2.5 26.4 1.0 O A:HOH211 2.5 24.5 1.0 N7 A:G9 2.6 29.0 1.0 C8 A:G9 3.3 30.1 1.0 C5 A:G9 3.6 33.2 1.0 OP2 A:A8 3.9 24.4 1.0 O6 A:G9 4.0 28.0 1.0 N7 A:G10 4.0 29.3 1.0 C6 A:G9 4.2 31.6 1.0 OP2 A:A7 4.2 26.8 1.0 OP2 A:G9 4.3 31.1 1.0 O6 A:G10 4.3 30.4 1.0 O A:HOH202 4.4 23.4 1.0 N7 A:A8 4.4 30.8 1.0 N9 A:G9 4.6 30.2 1.0 O4 B:U18 4.6 28.0 1.0 C5 A:A8 4.7 30.5 1.0 C4 A:G9 4.7 31.0 1.0 O B:HOH228 4.8 29.8 1.0 C5 A:G10 4.8 31.2 1.0 C5' A:A7 4.9 29.5 1.0 C8 A:G10 4.9 31.4 1.0 N6 A:A8 4.9 24.3 1.0 C6 A:A8 4.9 29.0 1.0 C8 A:A8 4.9 27.6 1.0 C6 A:G10 5.0 30.4 1.0

Manganese binding site 2 out of 22 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 Manganese with other atoms in the Mn 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:Mn102 b:66.2 occ:1.00 O6 A:G16 4.1 38.4 1.0 N7 A:G16 4.3 41.1 1.0 O6 A:G17 4.5 43.7 1.0 N4 A:C15 4.5 35.6 1.0 C6 A:G16 4.8 37.9 1.0 N4 B:C2 4.9 40.8 1.0 C5 A:G16 4.9 41.5 1.0 C5 A:C15 5.0 40.2 1.0 C4 A:C15 5.0 37.0 1.0

Manganese binding site 3 out of 22 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 Manganese with other atoms in the Mn 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:Mn101 b:53.1 occ:1.00 O B:HOH254 2.2 33.3 1.0 O A:HOH224 2.5 23.9 1.0 O A:HOH210 2.7 33.4 1.0 O6 A:G5 4.4 32.0 1.0 N7 A:G5 4.5 37.0 1.0 OP1 B:C42 4.6 30.1 1.0 C3' B:G41 4.9 27.9 1.0 O2' B:G41 4.9 27.7 1.0 O3' B:G41 5.0 34.2 1.0

Manganese binding site 4 out of 22 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 Manganese with other atoms in the Mn 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:Mn102 b:35.7 occ:1.00 OP2 B:C42 2.1 27.0 1.0 OP2 B:U43 2.1 25.8 1.0 O B:HOH217 2.5 30.3 1.0 P B:U43 3.5 27.6 1.0 P B:C42 3.5 28.8 1.0 O B:HOH221 3.7 30.3 1.0 OP1 B:U43 4.1 28.8 1.0 OP1 B:C42 4.1 30.1 1.0 O3' B:C42 4.2 25.8 1.0 O5' B:C42 4.2 27.0 1.0 OP2 B:A45 4.3 38.9 1.0 O A:HOH210 4.4 33.4 1.0 C5' B:C42 4.5 27.5 1.0 O3' B:G41 4.6 34.2 1.0 C3' B:C42 4.6 29.0 1.0 O5' B:U43 4.6 28.7 1.0 O B:HOH281 4.8 28.9 1.0 O6 A:G5 4.9 32.0 1.0

Manganese binding site 5 out of 22 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 Manganese with other atoms in the Mn 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:Mn103 b:38.6 occ:1.00 O B:HOH237 2.0 31.7 1.0 OP1 B:U43 2.2 28.8 1.0 OP2 B:DC44 2.3 31.1 1.0 P B:U43 3.5 27.6 1.0 P B:DC44 3.7 33.3 1.0 C5' B:DC44 4.0 33.3 1.0 O5' B:U43 4.0 28.7 1.0 C5' B:U43 4.1 29.0 1.0 O B:HOH281 4.3 28.9 1.0 OP2 B:U43 4.4 25.8 1.0 O5' B:DC44 4.4 39.9 1.0 OP1 B:DC44 4.5 37.1 1.0 O3' B:C42 4.6 25.8 1.0 O3' B:U43 4.7 32.6 1.0

Manganese binding site 6 out of 22 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 Manganese with other atoms in the Mn 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:Mn104 b:60.3 occ:1.00 O B:HOH289 2.3 41.9 1.0 N7 B:G47 2.4 42.7 1.0 O B:HOH208 2.4 41.0 1.0 O B:HOH298 2.5 49.8 1.0 O B:HOH259 2.6 38.2 1.0 O B:HOH275 2.7 51.6 1.0 C8 B:G47 3.3 40.2 1.0 C5 B:G47 3.4 39.6 1.0 O6 B:G47 3.5 42.3 1.0 C6 B:G47 3.8 42.6 1.0 OP2 B:U46 4.2 33.1 1.0 OP1 B:A45 4.3 38.3 1.0 N2 A:G5 4.5 35.8 1.0 N9 B:G47 4.5 43.3 1.0 C4 B:G47 4.6 39.8 1.0 O3' B:DC44 5.0 43.5 1.0

Manganese binding site 7 out of 22 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 Manganese with other atoms in the Mn 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:Mn105 b:65.5 occ:1.00 O D:HOH223 2.2 33.0 1.0 O B:HOH284 2.5 34.1 1.0 N1 B:A45 2.8 27.3 1.0 O2 B:C14 3.0 36.1 1.0 N6 B:A45 3.5 29.2 1.0 C6 B:A45 3.5 30.9 1.0 C2 B:A45 3.6 34.1 1.0 N3 B:C14 3.7 37.5 1.0 C2 B:C14 3.7 34.6 1.0 O A:HOH220 4.0 37.1 1.0 O2' B:U46 4.1 30.1 1.0 O B:HOH253 4.3 38.0 1.0 OP1 D:C5 4.4 43.7 1.0 OP2 D:C5 4.6 31.0 1.0 C1' B:U46 4.7 30.9 1.0 C5 B:A45 4.7 31.6 1.0 N3 B:A45 4.8 31.8 1.0 C4 B:C14 4.9 34.4 1.0 P D:C5 4.9 36.1 1.0

Manganese binding site 8 out of 22 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 Manganese with other atoms in the Mn 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:Mn106 b:40.0 occ:1.00 O A:HOH216 2.2 29.2 1.0 O6 B:G41 2.4 30.3 1.0 O B:HOH280 2.5 32.7 1.0 O B:HOH264 2.6 30.0 1.0 O B:HOH267 2.6 31.6 1.0 O B:HOH272 2.6 33.1 1.0 C6 B:G41 3.5 32.5 1.0 N7 B:G41 4.2 31.3 1.0 C5 B:G41 4.2 31.0 1.0 O A:HOH225 4.3 33.8 1.0 OP2 B:C40 4.3 30.0 1.0 O2 B:U18 4.4 28.5 1.0 O B:HOH244 4.5 29.0 1.0 C5 B:C40 4.5 28.6 1.0 OP2 B:G39 4.5 27.5 1.0 OP1 A:C6 4.6 30.3 1.0 N1 B:G41 4.6 27.6 1.0 O B:HOH216 4.6 32.5 1.0 O A:HOH217 4.7 31.3 1.0 O A:HOH203 4.8 28.9 1.0

Manganese binding site 9 out of 22 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 Manganese with other atoms in the Mn 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:Mn107 b:33.5 occ:1.00 O B:HOH246 2.0 26.2 1.0 OP1 B:G38 2.0 31.1 1.0 O B:HOH274 2.1 27.9 1.0 OP1 B:G7 2.3 28.8 1.0 O B:HOH220 2.5 30.0 1.0 O B:HOH255 2.5 27.9 1.0 P B:G38 3.4 38.5 1.0 P B:G7 3.5 32.5 1.0 O3' B:C6 3.9 31.2 1.0 O3' B:G37 4.0 37.0 1.0 OP2 B:G38 4.0 37.9 1.0 N7 B:G7 4.2 40.9 1.0 C3' B:G37 4.2 34.1 1.0 C8 B:G7 4.3 38.1 1.0 O2' B:G17 4.3 31.1 1.0 OP2 B:G7 4.3 34.7 1.0 C2' B:G37 4.3 34.9 1.0 O2' B:C6 4.4 33.2 1.0 C3' B:C6 4.5 32.2 1.0 O5' B:G38 4.5 30.2 1.0 C5' B:U18 4.5 23.6 1.0 O5' B:G7 4.8 29.6 1.0 O B:HOH223 4.9 38.0 1.0 C5' B:G7 4.9 31.1 1.0 C4' B:U18 4.9 27.5 1.0

Manganese binding site 10 out of 22 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 Manganese with other atoms in the Mn 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:Mn108 b:32.7 occ:1.00 O A:HOH207 2.0 27.2 1.0 O A:HOH202 2.3 23.4 1.0 O A:HOH222 2.4 28.1 1.0 N7 B:G17 2.4 28.3 1.0 O B:HOH293 2.5 25.8 1.0 O B:HOH290 2.6 28.4 1.0 C8 B:G17 3.2 28.3 1.0 C5 B:G17 3.5 29.3 1.0 O6 B:G17 3.8 30.3 1.0 OP1 A:A8 4.0 27.5 1.0 C6 B:G17 4.1 33.9 1.0 OP2 A:A8 4.2 24.4 1.0 O B:HOH260 4.3 33.8 1.0 O4 B:U18 4.4 28.0 1.0 OP1 B:G17 4.4 31.6 1.0 N9 B:G17 4.5 32.6 1.0 C4 B:G17 4.6 33.0 1.0 P A:A8 4.7 29.1 1.0 O A:HOH201 4.7 27.8 1.0 C5 B:U18 4.9 26.3 1.0 OP2 A:G9 4.9 31.1 1.0 C4 B:U18 5.0 26.1 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