Magnesium in PDB 6tpq: Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna

All present enzymatic activity of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna:
3.1.26.8;

The structure of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 219;

Binding sites:

The binding sites of Magnesium atom in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna (pdb code 6tpq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 219 binding sites of Magnesium where determined in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna, PDB code: 6tpq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg201 b:0.5 occ:1.00 OP2 V:G98 2.0 0.3 1.0 P V:G98 3.0 0.3 1.0 O5' V:G98 3.5 0.3 1.0 OP1 V:G98 3.5 0.3 1.0 OP2 V:A99 4.1 0.4 1.0 O3' V:A97 4.4 0.4 1.0 O6 V:G100 4.4 0.7 1.0 N7 V:A99 4.5 0.4 1.0 C5' V:G98 4.8 0.3 1.0 C3' V:A97 4.9 0.4 1.0 OP2 V:A71 5.0 1.0 1.0

Magnesium binding site 2 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3001 b:0.6 occ:1.00 OP2 U:G13 2.0 0.2 1.0 OP1 U:G13 2.2 0.2 1.0 P U:G13 2.2 0.2 1.0 O5' U:G13 2.9 0.2 1.0 C5' U:G13 3.2 0.2 1.0 O3' U:A12 3.8 0.8 1.0 OP2 U:A12 4.2 0.8 1.0 C3' U:A12 4.6 0.8 1.0 C4' U:G13 4.7 0.2 1.0 C5' U:A12 4.9 0.8 1.0 O5' U:A12 5.0 0.8 1.0

Magnesium binding site 3 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3002 b:79.5 occ:1.00 O6 U:G519 4.5 1.0 1.0 O6 U:G28 4.5 0.9 1.0 N4 U:C29 4.6 1.0 1.0 OP2 U:A26 4.7 0.2 1.0 O6 U:G518 4.8 0.4 1.0 O4 U:U27 4.8 0.5 1.0 OP2 U:A492 4.8 0.1 1.0 C5 U:U27 4.9 0.5 1.0

Magnesium binding site 4 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3003 b:0.6 occ:1.00 OP1 U:C29 2.0 1.0 1.0 P U:C29 3.3 1.0 1.0 OP1 U:C1277 3.7 0.1 1.0 O3' U:G28 3.9 0.9 1.0 OP2 U:C29 3.9 1.0 1.0 O5' U:C29 4.5 1.0 1.0 OP1 U:C1239 4.5 0.3 1.0 C5' U:C29 4.8 1.0 1.0 C5' U:C1277 4.8 0.1 1.0

Magnesium binding site 5 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3004 b:0.2 occ:1.00 O6 U:G80 3.6 0.4 1.0 C6 U:G80 4.6 0.4 1.0 OP1 U:A100 4.6 0.5 1.0 N1 U:G80 4.7 0.4 1.0 N7 U:G78 4.7 0.6 1.0 O6 U:G79 4.8 0.7 1.0 N7 U:G79 4.9 0.7 1.0

Magnesium binding site 6 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3005 b:1.0 occ:1.00 OP2 U:U117 1.9 0.1 1.0 P U:U117 3.2 0.1 1.0 O5' U:U117 3.5 0.1 1.0 O3' U:A116 3.8 0.2 1.0 O6 U:G120 4.3 0.5 1.0 OP1 U:G118 4.4 0.3 1.0 OP1 U:U117 4.4 0.1 1.0 O2' U:A116 4.5 0.2 1.0 O6 U:G119 4.5 0.2 1.0 C5' U:U117 4.9 0.1 1.0 C3' U:A116 4.9 0.2 1.0 O6 U:G121 4.9 0.3 1.0 N7 U:G119 5.0 0.2 1.0 C3' U:U117 5.0 0.1 1.0

Magnesium binding site 7 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3006 b:0.3 occ:1.00 OP2 U:G118 2.0 0.3 1.0 P U:G118 3.3 0.3 1.0 O6 U:G49 3.8 0.8 1.0 OP2 U:U147 3.8 0.7 1.0 O3' U:U117 3.9 0.1 1.0 O2' U:U117 3.9 0.1 1.0 OP1 U:G118 4.1 0.3 1.0 O5' U:G118 4.5 0.3 1.0 OP2 U:A148 4.7 0.8 1.0 C5' U:G118 4.8 0.3 1.0 C6 U:G49 4.8 0.8 1.0 C2' U:U117 4.9 0.1 1.0 C3' U:U117 4.9 0.1 1.0

Magnesium binding site 8 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3007 b:0.5 occ:1.00 OP2 U:A176 2.0 0.7 1.0 OP1 U:G175 2.0 0.3 1.0 P U:G175 3.1 0.3 1.0 P U:A176 3.3 0.7 1.0 O3' U:A174 3.4 0.6 1.0 O5' U:G175 3.5 0.3 1.0 OP1 U:A176 3.9 0.7 1.0 O3' U:G175 4.0 0.3 1.0 C3' U:G175 4.3 0.3 1.0 O5' U:A176 4.4 0.7 1.0 OP2 U:G175 4.5 0.3 1.0 C3' U:A174 4.8 0.6 1.0 C5' U:G175 4.8 0.3 1.0 N1 U:A177 4.9 1.0 1.0

Magnesium binding site 9 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3008 b:0.0 occ:1.00 N7 U:G178 4.1 0.8 1.0 O6 U:G178 4.2 0.8 1.0 OP1 U:A177 4.3 1.0 1.0 O6 U:G179 4.3 0.4 1.0 N7 U:G179 4.5 0.4 1.0 C5 U:G178 4.7 0.8 1.0 C6 U:G178 4.7 0.8 1.0 OP2 U:A214 4.9 0.1 1.0 C8 U:G178 5.0 0.8 1.0

Magnesium binding site 10 out of 219 in the Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Rnase M5 Bound to 50S Ribosome with Precursor 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg3009 b:0.9 occ:1.00 OP2 U:G189 3.5 0.2 1.0 OP2 U:G188 3.6 0.6 1.0 O6 U:G190 4.1 0.1 1.0 N7 U:G190 4.5 0.1 1.0 P U:G188 4.5 0.6 1.0 N7 U:G189 4.6 0.2 1.0 O5' U:G188 4.6 0.6 1.0 C8 U:G189 4.7 0.2 1.0 P U:G189 4.8 0.2 1.0 C6 U:G190 4.9 0.1 1.0

S.Oerum, T.Dendooven, M.Catala, L.Gilet, C.Degut, A.Trinquier, M.Bourguet, P.Barraud, S.Cianferani, B.F.Luisi, C.Condon, C.Tisne. Structures of B. Subtilis Maturation Rnases Captured on 50S Ribosome with Pre-Rrnas. Mol.Cell V. 80 227 2020.
ISSN: ISSN 1097-2765
PubMed: 32991829
DOI: 10.1016/J.MOLCEL.2020.09.008