Magnesium in PDB 8ana: Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit

The structure of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit 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 - 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 - 216;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit (pdb code 8ana). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 216 binding sites of Magnesium where determined in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit, PDB code: 8ana:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6001 b:34.3 occ:1.00 O6 a:G474 4.0 24.0 1.0 OP2 a:A28 4.1 18.5 1.0 O4 a:U29 4.2 18.8 1.0 O6 a:G30 4.3 17.6 1.0 OP2 a:A447 4.3 22.1 1.0 C5 a:U29 4.3 18.5 1.0 O6 a:G473 4.5 26.0 1.0 N4 a:C31 4.5 20.1 1.0 OP2 a:U29 4.6 18.4 1.0 C4 a:U29 4.6 18.3 1.0

Magnesium binding site 2 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6002 b:28.3 occ:1.00 OP2 a:U120 2.0 26.4 1.0 P a:U120 3.4 24.9 1.0 N7 a:G122 4.1 23.0 1.0 OP1 a:U120 4.1 26.7 1.0 O3' a:A119 4.2 24.6 1.0 O6 a:G122 4.3 23.6 1.0 O6 a:G123 4.4 21.9 1.0 O5' a:U120 4.4 25.4 1.0 OP1 a:G121 4.5 27.5 1.0 N7 a:G121 4.5 28.0 1.0 C5' a:U120 4.6 25.4 1.0 OP2 a:G122 4.6 25.9 1.0 C5 a:G121 4.9 27.6 1.0 C5 a:G122 4.9 23.2 1.0 C3' a:U120 4.9 25.8 1.0 C6 a:G122 4.9 23.2 1.0 C8 a:G121 5.0 27.8 1.0

Magnesium binding site 3 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6003 b:30.2 occ:1.00 OP1 a:U120 2.0 26.7 1.0 P a:U120 3.4 24.9 1.0 OP2 a:G123 3.9 23.1 1.0 O5' a:U120 4.0 25.4 1.0 O6 a:G124 4.2 21.9 1.0 OP2 a:U120 4.2 26.4 1.0 C5' a:U120 4.3 25.4 1.0 OP2 a:G122 4.5 25.9 1.0 O3' a:A119 4.5 24.6 1.0 N7 a:G123 4.6 21.6 1.0 C3' a:A119 4.7 23.5 1.0 C5' a:A119 5.0 23.9 1.0

Magnesium binding site 4 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6004 b:41.9 occ:1.00 OP2 a:A218 2.0 37.5 1.0 P a:A218 3.4 35.7 1.0 N6 a:A219 3.9 31.2 1.0 O5' a:A218 4.0 36.3 1.0 N7 a:A218 4.1 34.5 1.0 OP1 a:A218 4.2 36.9 1.0 C8 a:A218 4.3 34.5 1.0 N7 a:A219 4.4 31.5 1.0 O5' a:A217 4.4 34.2 1.0 O6 a:G220 4.4 33.6 1.0 OP1 a:A428 4.4 44.2 1.0 O3' a:A217 4.5 35.6 1.0 OP1 a:A217 4.5 35.1 1.0 C3' a:A217 4.6 34.5 1.0 OP2 a:A217 4.7 34.8 1.0 P a:A217 4.7 34.6 1.0 OP2 a:U427 4.8 42.6 1.0 C6 a:A219 4.9 31.1 1.0 C5' a:A217 4.9 34.2 1.0 C5 a:A219 5.0 31.1 1.0

Magnesium binding site 5 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6005 b:38.1 occ:1.00 OP1 a:U419 2.0 34.1 1.0 P a:U419 3.4 32.2 1.0 O3' a:C418 4.0 32.1 1.0 C5' a:U419 4.0 31.4 1.0 O5' a:U419 4.2 32.2 1.0 N7 a:G230 4.2 37.1 1.0 OP2 a:U419 4.5 33.5 1.0 C8 a:G230 4.8 37.5 1.0

Magnesium binding site 6 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6006 b:19.0 occ:1.00 OP2 a:G450 2.0 17.1 1.0 P a:G450 3.4 16.4 1.0 OP2 a:G452 3.8 19.3 1.0 O5' a:G450 3.9 16.8 1.0 O e:GLY81 4.0 17.4 1.0 OP2 a:U451 4.0 19.1 1.0 OP1 a:G450 4.2 17.0 1.0 O e:SER80 4.4 17.5 1.0 OP1 a:A449 4.4 17.0 1.0 O3' a:A449 4.5 16.4 1.0 C e:SER80 4.6 17.1 1.0 CA e:SER80 4.8 16.8 1.0 C3' a:A449 4.8 16.1 1.0 OP2 a:A449 4.9 16.5 1.0 O5' a:A449 4.9 16.6 1.0 CG2 e:VAL52 4.9 23.8 1.0 P a:A449 4.9 16.5 1.0

Magnesium binding site 7 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6007 b:17.1 occ:1.00 OP1 a:A453 2.0 17.1 1.0 O6 a:G450 2.0 16.1 1.0 C6 a:G450 3.1 15.8 1.0 P a:A453 3.4 16.9 1.0 C5 a:G450 3.8 15.9 1.0 N7 a:G450 3.8 16.0 1.0 OP2 a:A453 4.0 17.2 1.0 O5' a:A453 4.1 17.8 1.0 N7 a:A449 4.1 14.9 1.0 N1 a:G450 4.3 15.9 1.0 C5' a:A453 4.3 18.6 1.0 OP1 a:A454 4.3 21.3 1.0 OP2 a:A449 4.4 16.5 1.0 O3' a:G452 4.5 17.5 1.0 N6 a:A449 4.5 15.1 1.0 C5' a:U448 4.8 18.9 1.0 C5 a:A449 4.9 15.0 1.0 C8 a:A449 5.0 15.0 1.0

Magnesium binding site 8 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6008 b:22.3 occ:1.00 OP1 a:A526 2.0 22.4 1.0 OP1 a:C527 2.0 21.2 1.0 P a:A526 3.4 21.3 1.0 P a:C527 3.4 19.8 1.0 OP2 a:A526 4.0 21.8 1.0 OP2 a:C527 4.1 20.5 1.0 O5' a:A526 4.1 21.3 1.0 OP1 a:A528 4.2 23.2 1.0 O5' a:C527 4.3 20.8 1.0 C5' a:A526 4.5 20.8 1.0 O3' a:A526 4.5 20.6 1.0 O3' a:U525 4.5 21.8 1.0 C5' a:C527 4.6 20.8 1.0 C3' a:A526 4.8 20.4 1.0 C3' a:C527 4.9 21.4 1.0

Magnesium binding site 9 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6009 b:59.9 occ:1.00 OP2 a:C560 3.9 20.6 1.0 OP1 a:A1008 4.0 20.6 1.0 OP1 a:C560 4.0 20.5 1.0 OP1 a:G559 4.3 21.9 1.0 P a:C560 4.3 20.4 1.0 OP1 a:G2038 4.4 16.3 1.0 O3' a:G559 5.0 20.5 1.0

Magnesium binding site 10 out of 216 in the Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of the Proline-Rich Antimicrobial Peptide Drosocin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg6010 b:16.7 occ:1.00 OP1 a:U567 2.0 15.1 1.0 P a:U567 3.3 14.4 1.0 O3' a:U566 3.7 14.3 1.0 OP2 a:G808 4.1 13.7 1.0 C5' a:U567 4.1 14.6 1.0 O4 a:U810 4.2 13.7 1.0 O5' a:U567 4.2 14.6 1.0 N7 a:G809 4.2 12.6 1.0 OP2 a:G809 4.3 13.1 1.0 OP2 a:U567 4.4 14.5 1.0 ND1 k:HIS35 4.7 20.4 1.0 C8 a:G809 4.8 12.5 1.0

T.O.Koller, M.Morici, M.J.Berger, H.Safdari, D.S.Lele, B.Beckert, K.J.Kaur, D.N.Wilson. Structural Basis For Translation Inhibition By the Glycosylated Antimicrobial Peptide Drosocin From Drosophila Melanogaster To Be Published 2023.
DOI: 10.1038/S41589-023-01293-7