Magnesium in PDB 7qq3: Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.

The structure of Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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 - 145;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. (pdb code 7qq3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 145 binding sites of Magnesium where determined in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A., PDB code: 7qq3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3001 b:50.1 occ:1.00 O4 I:U18 4.1 44.5 1.0 O6 I:G17 4.2 44.5 1.0 N7 I:G17 4.3 44.5 1.0 O4 I:U521 4.6 50.4 1.0 N4 I:C16 4.7 44.5 1.0 C6 I:G17 4.9 44.5 1.0 C5 I:G17 4.9 44.5 1.0 N6 I:A522 5.0 50.1 1.0

Magnesium binding site 2 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3002 b:44.7 occ:1.00 O6 I:G474 4.1 47.1 1.0 O4 I:U29 4.3 42.5 1.0 O6 I:G30 4.4 44.6 1.0 OP2 I:A28 4.4 41.2 1.0 O6 I:G473 4.5 45.3 1.0 C5 I:U29 4.5 42.5 1.0 OP2 I:A447 4.6 43.6 1.0 N4 I:C31 4.7 46.3 1.0 C4 I:U29 4.7 42.5 1.0 OP2 I:U29 4.9 42.5 1.0

Magnesium binding site 3 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3003 b:50.9 occ:1.00 OP2 I:U120 2.1 51.3 1.0 P I:U120 3.5 51.3 1.0 OP1 I:G121 4.2 53.9 1.0 O3' I:A119 4.2 48.5 1.0 OP1 I:U120 4.2 51.3 1.0 N7 I:G122 4.3 50.0 1.0 O5' I:U120 4.4 51.3 1.0 O6 I:G122 4.5 50.0 1.0 C5' I:U120 4.5 51.3 1.0 O6 I:G123 4.5 47.0 1.0 N7 I:G121 4.6 53.9 1.0 OP2 I:G122 4.8 50.0 1.0 C3' I:U120 4.9 51.3 1.0

Magnesium binding site 4 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3004 b:52.0 occ:1.00 OP1 I:U120 1.9 51.3 1.0 P I:U120 3.2 51.3 1.0 O5' I:U120 3.8 51.3 1.0 OP2 I:U120 4.0 51.3 1.0 OP2 I:G123 4.1 47.0 1.0 C5' I:U120 4.2 51.3 1.0 O6 I:G124 4.3 45.0 1.0 O3' I:A119 4.4 48.5 1.0 N7 I:G123 4.6 47.0 1.0 C3' I:A119 4.6 48.5 1.0 OP2 I:G122 4.7 50.0 1.0 C4' I:A119 5.0 48.5 1.0

Magnesium binding site 5 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3005 b:56.3 occ:1.00 OP2 I:A218 2.1 53.4 1.0 P I:A218 3.4 53.4 1.0 O5' I:A218 4.0 53.4 1.0 N6 I:A219 4.1 56.0 1.0 OP1 I:A218 4.2 53.4 1.0 N7 I:A218 4.3 53.4 1.0 N7 I:A219 4.3 56.0 1.0 C8 I:A218 4.4 53.4 1.0 O6 I:G220 4.5 58.3 1.0 O3' I:A217 4.6 53.2 1.0 O5' I:A217 4.7 53.2 1.0 C3' I:A217 4.8 53.2 1.0 OP1 I:A428 4.9 60.5 1.0 OP2 I:U427 5.0 60.6 1.0

Magnesium binding site 6 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3006 b:56.3 occ:1.00 OP1 I:U419 2.2 55.3 1.0 P I:U419 3.6 55.3 1.0 O3' I:C418 4.0 54.6 1.0 N7 I:G230 4.0 56.9 1.0 C5' I:U419 4.1 55.3 1.0 O5' I:U419 4.3 55.3 1.0 C8 I:G230 4.5 56.9 1.0 OP2 I:U419 4.7 55.3 1.0

Magnesium binding site 7 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3007 b:42.9 occ:1.00 OP2 I:G450 2.1 41.5 1.0 P I:G450 3.4 41.5 1.0 N M:GLY81 3.8 41.9 1.0 OP2 I:G452 3.9 42.1 1.0 O5' I:G450 4.0 41.5 1.0 OP1 I:G450 4.2 41.5 1.0 OP2 I:U451 4.3 42.7 1.0 CA M:GLY81 4.3 41.9 1.0 OP1 I:A449 4.5 41.4 1.0 O3' I:A449 4.5 41.4 1.0 OP2 I:A449 4.8 41.4 1.0 C M:SER80 4.8 41.1 1.0 C3' I:A449 4.9 41.4 1.0 CA M:SER80 4.9 41.1 1.0 P I:A449 5.0 41.4 1.0

Magnesium binding site 8 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3008 b:41.4 occ:1.00 OP1 I:A453 1.9 42.6 1.0 O6 I:G450 2.0 41.5 1.0 C6 I:G450 3.2 41.5 1.0 P I:A453 3.3 42.6 1.0 O5' I:A453 3.9 42.6 1.0 C5 I:G450 3.9 41.5 1.0 N7 I:G450 4.0 41.5 1.0 OP2 I:A453 4.0 42.6 1.0 C5' I:A453 4.1 42.6 1.0 N1 I:G450 4.2 41.5 1.0 O3' I:G452 4.4 42.1 1.0 OP1 I:A454 4.4 43.7 1.0 N7 I:A449 4.5 41.4 1.0 OP2 I:A449 4.7 41.4 1.0 N6 I:A449 4.8 41.4 1.0

Magnesium binding site 9 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3009 b:51.7 occ:1.00 OP1 I:C560 4.1 42.6 1.0 OP1 I:A1008 4.2 45.7 1.0 OP2 I:C560 4.4 42.6 1.0 OP1 I:G2038 4.4 38.2 1.0 OP1 I:G559 4.7 45.0 1.0 P I:C560 4.8 42.6 1.0

Magnesium binding site 10 out of 145 in the Cryo-Em Structure of the E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A.


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 E.Coli 50S Ribosomal Subunit in Complex with the Antibiotic Myxovalargin A. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg3010 b:38.5 occ:1.00 OP1 I:U567 2.1 35.4 1.0 P I:U567 3.4 35.4 1.0 O3' I:U566 3.9 35.5 1.0 C5' I:U567 4.1 35.4 1.0 OP2 I:G808 4.2 34.7 1.0 O5' I:U567 4.2 35.4 1.0 OP2 I:G809 4.5 35.0 1.0 OP2 I:U567 4.6 35.4 1.0 N7 I:G809 4.6 35.0 1.0 O4 I:U810 4.6 36.0 1.0 ND1 T:HIS35 4.7 37.1 1.0

T.O.Koller, U.Scheid, T.Kosel, J.Herrmann, D.Krug, H.I.M.Boshoff, B.Beckert, J.C.Evans, J.Schlemmer, B.Sloan, D.M.Weiner, L.E.Via, A.Moosa, T.R.Ioerger, M.Graf, B.Zinshteyn, M.Abdelshahid, F.Nguyen, S.Arenz, F.Gille, M.Siebke, T.Seedorf, O.Plettenburg, R.Green, A.L.Warnke, J.Ullrich, R.Warrass, C.E.Barry 3Rd, D.F.Warner, V.Mizrahi, A.Kirschning, D.N.Wilson, R.Muller. The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 36603206
DOI: 10.1021/JACS.2C08816