Magnesium in PDB 4v19: Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2

The structure of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 also contains other interesting chemical elements:

Zinc

(Zn)

2 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 - 169;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 (pdb code 4v19). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 169 binding sites of Magnesium where determined in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2, PDB code: 4v19:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2570 b:6.5 occ:1.00 OP1 A:A1324 2.7 18.0 1.0 OP1 A:C1322 3.0 16.6 1.0 O3' A:A191 3.2 8.9 1.0 OP1 A:U192 3.3 17.7 1.0 O3' A:U1321 3.3 10.0 1.0 OP1 A:U1325 3.5 19.1 1.0 OP2 A:U1325 3.8 34.3 1.0 P A:C1322 3.8 14.1 1.0 P A:U192 3.9 16.5 1.0 P A:A1324 4.0 26.1 1.0 P A:U1325 4.2 24.7 1.0 O2' A:U1321 4.2 13.7 1.0 MG A:MG2595 4.2 4.0 1.0 O2' A:A191 4.3 11.3 1.0 O5' A:A1324 4.3 21.5 1.0 C3' A:A191 4.4 7.6 1.0 C5' A:U192 4.4 8.0 1.0 C5' A:C1322 4.5 7.8 1.0 C3' A:U1321 4.5 7.2 1.0 C4' A:A191 4.5 9.8 1.0 O5' A:U192 4.6 11.9 1.0 O5' A:C1322 4.7 9.9 1.0 C4' A:U1321 4.8 7.8 1.0 OP2 A:A1324 4.8 20.5 1.0 C5' A:A1324 4.8 18.7 1.0 C2' A:U1321 5.0 8.1 1.0 C2' A:A191 5.0 7.9 1.0

Magnesium binding site 2 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2571 b:0.0 occ:1.00 OP1 A:A1026 2.1 18.7 1.0 O4 A:U1021 2.5 9.2 1.0 P A:A1026 3.6 24.3 1.0 C4 A:U1021 3.7 7.0 1.0 O6 A:G1022 4.0 9.1 1.0 O6 A:G1020 4.1 11.2 1.0 N7 A:G1020 4.1 7.0 1.0 O3' A:G1025 4.3 24.1 1.0 C5 A:U1021 4.4 8.2 1.0 O5' A:A1026 4.5 14.6 1.0 OP2 A:A1026 4.5 18.2 1.0 C8 A:A1026 4.5 7.8 1.0 N3 A:U1021 4.7 5.8 1.0 C6 A:G1020 4.7 8.3 1.0 C6 A:G1022 4.7 7.0 1.0 C5 A:G1020 4.7 6.4 1.0 N1 A:G1022 4.9 6.0 1.0 C2' A:A1026 5.0 10.6 1.0

Magnesium binding site 3 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2572 b:8.1 occ:1.00 O4 A:U752 2.2 23.7 1.0 OP1 A:A704 2.2 22.6 1.0 C4 A:U752 3.3 23.1 1.0 P A:A704 3.6 30.8 1.0 O X:THR70 3.8 22.9 1.0 C5 A:U752 4.0 21.8 1.0 O5' A:A704 4.2 24.7 1.0 O4 A:U750 4.2 28.3 1.0 O6 A:G751 4.2 27.7 1.0 OP2 A:A704 4.3 28.5 1.0 N7 A:G751 4.4 18.5 1.0 C4 A:U750 4.4 28.1 1.0 N3 A:U752 4.5 17.8 1.0 NH2 X:ARG50 4.5 25.5 1.0 C5 A:U750 4.5 30.3 1.0 C4' A:U703 4.6 18.2 1.0 C5' A:U703 4.7 20.2 1.0 O3' A:U703 4.8 17.1 1.0 C8 A:A704 4.8 23.8 1.0 C3' A:U703 4.9 14.1 1.0 C X:THR70 5.0 19.1 1.0

Magnesium binding site 4 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2573 b:0.7 occ:1.00 OP1 A:C287 2.3 16.6 1.0 P A:C287 3.7 24.6 1.0 O3' A:G1428 3.7 23.4 1.0 OP1 A:G1429 4.0 50.9 1.0 O3' A:U286 4.2 16.7 1.0 C4' A:G1428 4.3 15.7 1.0 OP1 A:G976 4.4 38.2 1.0 C5' A:G1428 4.4 18.6 1.0 C5' A:C287 4.5 11.8 1.0 P A:G1429 4.5 33.4 1.0 OP2 A:G976 4.6 35.8 1.0 O5' A:C287 4.6 15.2 1.0 C3' A:G1428 4.6 15.2 1.0 OP2 A:C287 4.7 35.5 1.0 C5' A:A834 4.8 16.3 1.0 P A:G976 4.9 36.7 1.0 OP1 A:A835 4.9 22.6 1.0

Magnesium binding site 5 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2574 b:2.4 occ:1.00 OP1 A:U449 2.4 9.1 1.0 OP1 A:C1319 3.8 19.5 1.0 P A:U449 3.9 8.7 1.0 OP1 A:U433 3.9 50.0 1.0 O A:HOH5268 3.9 44.7 1.0 C5' A:U449 4.1 7.4 1.0 C5' A:A1318 4.3 14.4 1.0 O5' A:U449 4.4 7.1 1.0 OP2 A:U449 4.7 5.6 1.0 O3' A:C448 4.9 8.4 1.0

Magnesium binding site 6 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2575 b:18.9 occ:1.00 OP1 A:U1432 2.0 37.8 1.0 OP1 A:C1400 2.1 17.7 1.0 P A:U1432 3.3 44.9 1.0 P A:C1400 3.3 14.2 1.0 O5' A:C1400 3.6 14.5 1.0 OP2 A:U1432 3.7 46.0 1.0 O2' A:U1431 3.9 51.0 1.0 OP2 A:C1400 4.0 19.1 1.0 O2' A:G1397 4.0 19.3 1.0 OP2 A:U1401 4.1 25.5 1.0 O3' A:U1431 4.3 49.5 1.0 O5' A:U1432 4.3 28.0 1.0 O3' A:U1399 4.6 15.4 1.0 C5' A:C1400 4.7 14.1 1.0 C2' A:U1431 5.0 52.2 1.0

Magnesium binding site 7 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2576 b:0.0 occ:1.00 OP1 A:U183 1.9 5.2 1.0 NZ P:LYS48 2.8 10.1 1.0 P A:U183 3.3 6.3 1.0 O3' A:U182 3.8 6.5 1.0 OP2 A:U183 4.1 6.5 1.0 CD2 P:HIS53 4.1 8.1 1.0 NE2 P:HIS53 4.2 8.4 1.0 CE P:LYS48 4.3 7.2 1.0 OP2 A:G354 4.4 6.3 1.0 N7 A:G355 4.4 26.8 1.0 O4 A:U356 4.4 14.7 1.0 O5' A:U183 4.5 5.5 1.0 NE2 P:GLN58 4.5 10.9 1.0 OP1 A:G355 4.7 9.4 1.0 OE1 P:GLN58 4.7 8.5 1.0 C5' A:U183 4.8 5.5 1.0 CD P:LYS48 4.9 7.5 1.0

Magnesium binding site 8 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2577 b:0.8 occ:1.00 OP1 A:G376 2.3 7.8 1.0 P A:G376 3.8 8.1 1.0 N P:GLY55 4.2 5.1 1.0 O P:HIS53 4.3 11.2 1.0 CA P:GLY55 4.4 4.6 1.0 N7 A:A431 4.5 17.6 1.0 O5' A:G376 4.5 6.2 1.0 CB P:LYS54 4.5 5.1 1.0 OP1 A:U430 4.6 14.2 1.0 O3' A:A375 4.6 7.8 1.0 C5' A:G376 4.6 5.6 1.0 OP2 A:G376 4.7 15.3 1.0 C8 A:A431 4.9 20.6 1.0

Magnesium binding site 9 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2578 b:4.9 occ:1.00 OP1 A:A839 2.2 14.2 1.0 OP2 A:G867 3.6 25.1 1.0 P A:A839 3.7 14.1 1.0 OP2 A:C868 3.8 23.9 1.0 OP1 A:G867 3.9 23.4 1.0 P A:G867 4.1 21.8 1.0 O D:LEU275 4.2 20.7 1.0 O3' A:C838 4.4 10.8 1.0 OP2 A:A839 4.4 10.3 1.0 O5' A:G867 4.4 14.8 1.0 O D:SER273 4.6 11.5 1.0 O5' A:A839 4.8 7.1 1.0 C5 A:C868 4.9 14.2 1.0 CA D:TRP276 4.9 10.1 1.0 C D:LEU275 5.0 14.3 1.0 O D:GLY274 5.0 19.4 1.0 CD1 D:TRP276 5.0 14.1 1.0

Magnesium binding site 10 out of 169 in the Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome, Part 1 of 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2579 b:6.2 occ:1.00 OP1 A:G1409 2.2 68.9 1.0 OP1 A:A330 2.3 23.1 1.0 P A:G1409 3.5 49.1 1.0 P A:A330 3.7 18.6 1.0 OP2 A:G1409 4.0 28.3 1.0 O5' A:A330 4.1 20.8 1.0 OP2 A:A1410 4.2 23.0 1.0 C5' A:G1409 4.2 25.1 1.0 O6 A:G338 4.3 23.9 1.0 O5' A:G1409 4.4 26.3 1.0 O3' A:A329 4.6 17.0 1.0 O3' A:A1408 4.6 38.5 1.0 OP2 A:C1261 4.6 33.6 1.0 OP2 A:A330 4.7 14.9 1.0

B.J.Greber, D.Boehringer, M.Leibundgut, P.Bieri, A.Leitner, N.Schmitz, R.Aebersold, N.Ban. The Complete Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome Nature V. 515 283 2014.
ISSN: ISSN 0028-0836
PubMed: 25271403
DOI: 10.1038/NATURE13895