Magnesium in PDB 6xz7: E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).

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 - 178;

Binding sites:

The binding sites of Magnesium atom in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). (pdb code 6xz7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 178 binding sites of Magnesium where determined in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet)., PDB code: 6xz7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3001 b:30.0 occ:1.00 O A:HOH3697 1.8 30.0 1.0 O A:HOH3438 2.0 30.0 1.0 O A:HOH3693 2.2 30.0 1.0 O A:HOH3465 2.2 30.0 1.0 O A:HOH3231 2.5 30.0 1.0 O A:HOH3263 2.5 30.0 1.0 O4 A:U18 4.2 69.0 1.0 O4 A:U521 4.5 76.4 1.0 O6 A:G17 4.5 69.2 1.0 N7 A:G17 4.5 69.2 1.0

Magnesium binding site 2 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3002 b:30.0 occ:1.00 O A:HOH3612 1.7 30.0 1.0 O A:HOH3406 2.1 30.0 1.0 O A:HOH3321 2.2 30.0 1.0 O A:HOH3668 2.3 30.0 1.0 O A:HOH3486 2.3 30.0 1.0 O A:HOH3298 2.5 30.0 1.0 OP2 A:A28 4.2 66.8 1.0 O6 A:G474 4.3 74.4 1.0 OP2 A:A447 4.4 71.8 1.0 O6 A:G30 4.4 70.5 1.0 O4 A:U29 4.4 68.4 1.0 O6 A:G473 4.5 74.1 1.0 C5 A:U29 4.5 68.4 1.0 OP2 A:U29 4.6 68.4 1.0 N4 A:C31 4.7 72.3 1.0 C4 A:U29 4.8 68.4 1.0 O2' A:A447 5.0 71.8 1.0

Magnesium binding site 3 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3003 b:30.0 occ:1.00 O A:HOH3367 2.0 30.0 1.0 OP2 A:U120 2.1 81.4 1.0 O A:HOH3358 2.1 30.0 1.0 O A:HOH3542 2.3 30.0 1.0 O A:HOH3664 2.4 30.0 1.0 O A:HOH3237 2.6 30.0 1.0 P A:U120 3.5 81.4 1.0 N7 A:G122 4.0 77.8 1.0 O6 A:G123 4.1 73.9 1.0 O6 A:G122 4.2 77.8 1.0 O3' A:A119 4.2 77.4 1.0 OP1 A:U120 4.3 81.4 1.0 O5' A:U120 4.5 81.4 1.0 OP1 A:G121 4.5 83.2 1.0 OP2 A:G122 4.6 77.8 1.0 N7 A:G121 4.6 83.2 1.0 C5' A:U120 4.7 81.4 1.0 C5 A:G122 4.8 77.8 1.0 C6 A:G122 4.8 77.8 1.0 N7 A:G123 4.8 73.9 1.0 C5 A:G121 4.9 83.2 1.0 C6 A:G123 5.0 73.9 1.0 C8 A:G122 5.0 77.8 1.0

Magnesium binding site 4 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3004 b:30.0 occ:1.00 OP1 A:U419 1.8 84.2 1.0 P A:U419 3.3 84.2 1.0 O3' A:C418 3.9 83.8 1.0 C5' A:U419 4.0 84.2 1.0 O5' A:U419 4.0 84.2 1.0 OP2 A:U419 4.3 84.2 1.0 N7 A:G230 4.5 89.1 1.0

Magnesium binding site 5 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3005 b:30.0 occ:1.00 OP2 A:G450 1.9 67.9 1.0 O A:HOH3504 2.0 30.0 1.0 O A:HOH3377 2.1 30.0 1.0 O A:HOH3391 2.1 30.0 1.0 O A:HOH3301 2.2 30.0 1.0 O E:HOH301 2.2 30.0 1.0 P A:G450 3.3 67.9 1.0 O E:GLY81 3.7 65.0 1.0 OP2 A:G452 3.9 69.5 1.0 OP1 A:G450 4.0 67.9 1.0 O5' A:G450 4.1 67.9 1.0 OP1 A:A449 4.2 67.7 1.0 O E:SER80 4.2 64.6 1.0 OP2 A:U451 4.4 70.5 1.0 C E:SER80 4.4 64.6 1.0 O3' A:A449 4.4 67.7 1.0 CA E:SER80 4.5 64.6 1.0 C E:GLY81 4.7 65.0 1.0 O5' A:A449 4.7 67.7 1.0 P A:A449 4.7 67.7 1.0 OP2 A:A449 4.8 67.7 1.0 C3' A:A449 4.9 67.7 1.0

Magnesium binding site 6 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3006 b:30.0 occ:1.00 O6 A:G450 1.9 67.9 1.0 OP1 A:A453 2.1 69.8 1.0 O A:HOH3300 2.3 30.0 1.0 O A:HOH3390 2.3 30.0 1.0 O A:HOH3404 2.3 30.0 1.0 O A:HOH3627 2.4 30.0 1.0 C6 A:G450 3.0 67.9 1.0 P A:A453 3.4 69.8 1.0 C5 A:G450 3.8 67.9 1.0 N7 A:G450 3.8 67.9 1.0 O5' A:A453 4.1 69.8 1.0 N7 A:A449 4.1 67.7 1.0 OP2 A:A453 4.1 69.8 1.0 MG A:MG3106 4.1 30.0 1.0 N1 A:G450 4.2 67.9 1.0 OP1 A:A454 4.3 72.4 1.0 C5' A:A453 4.3 69.8 1.0 O3' A:G452 4.5 69.5 1.0 OP2 A:A449 4.5 67.7 1.0 N6 A:A449 4.6 67.7 1.0 C5' A:U448 4.9 68.1 1.0 C5 A:A449 4.9 67.7 1.0 C8 A:A449 4.9 67.7 1.0

Magnesium binding site 7 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3007 b:30.0 occ:1.00 OP1 A:U567 1.9 62.0 1.0 O A:HOH3297 2.2 30.0 1.0 O A:HOH3513 2.2 30.0 1.0 O A:HOH3593 2.3 30.0 1.0 O A:HOH3494 2.3 30.0 1.0 O L:HOH203 2.4 30.0 1.0 P A:U567 3.2 62.0 1.0 O3' A:U566 3.6 61.1 1.0 O5' A:U567 4.1 62.0 1.0 C5' A:U567 4.1 62.0 1.0 O A:HOH3595 4.1 30.0 1.0 O4 A:U810 4.2 60.3 1.0 OP2 A:G809 4.2 59.5 1.0 OP2 A:G808 4.3 59.5 1.0 OP2 A:U567 4.3 62.0 1.0 N7 A:G809 4.4 59.5 1.0 O L:HIS35 4.5 63.0 1.0 C3' A:U566 5.0 61.1 1.0

Magnesium binding site 8 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3008 b:30.0 occ:1.00 O A:HOH3675 2.2 30.0 1.0 O A:HOH3249 2.2 30.0 1.0 O A:HOH3294 2.3 30.0 1.0 O A:HOH3547 2.3 30.0 1.0 O A:HOH3424 2.3 30.0 1.0 O A:HOH3591 2.5 30.0 1.0 N4 A:C584 3.9 62.4 1.0 N7 A:G583 4.2 62.9 1.0 O2' A:C1251 4.3 62.4 1.0 OP2 A:A582 4.3 62.0 1.0 OP2 A:A1253 4.5 60.6 1.0 C5' A:G1252 4.6 61.5 1.0 N7 A:A582 4.6 62.0 1.0 O6 A:G585 4.7 61.8 1.0 O6 A:G583 4.7 62.9 1.0 OP2 A:G583 4.8 62.9 1.0 C4' A:G1252 4.9 61.5 1.0 C4 A:C584 5.0 62.4 1.0 C8 A:A582 5.0 62.0 1.0

Magnesium binding site 9 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3009 b:30.0 occ:1.00 O A:HOH3363 2.0 30.0 1.0 O A:HOH3689 2.1 30.0 1.0 O A:HOH3679 2.1 30.0 1.0 O A:HOH3442 2.4 30.0 1.0 O A:HOH3352 2.5 30.0 1.0 O A:HOH3255 2.5 30.0 1.0 OP2 A:A616 3.9 90.6 1.0 O6 A:G619 4.2 81.2 1.0 N7 A:G617 4.2 88.0 1.0 OP1 A:A616 4.3 90.6 1.0 CE E:LYS98 4.4 79.8 1.0 O6 A:G618 4.5 84.4 1.0 P A:A616 4.6 90.6 1.0 N7 A:G618 4.6 84.4 1.0 OP2 A:G617 4.7 88.0 1.0 O6 A:G617 4.8 88.0 1.0 OP2 A:A608 4.9 78.1 1.0 C6 A:G619 4.9 81.2 1.0

Magnesium binding site 10 out of 178 in the E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E. Coli 50S Ribosomal Subunit in Complex with Dirithromycin, Fmet-Phe- Trna(Phe) and Deacylated Trna(Imet). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3010 b:30.0 occ:1.00 O A:HOH3505 1.9 30.0 1.0 O A:HOH3384 2.0 30.0 1.0 N7 A:G733 2.1 66.3 1.0 N7 A:A761 2.2 64.4 1.0 O A:HOH3485 2.3 30.0 1.0 O A:HOH3433 2.4 30.0 1.0 C8 A:G733 2.9 66.3 1.0 C8 A:A761 3.1 64.4 1.0 C5 A:G733 3.2 66.3 1.0 C5 A:A761 3.3 64.4 1.0 O6 A:G733 3.6 66.3 1.0 N6 A:A761 3.7 64.4 1.0 C6 A:G733 3.8 66.3 1.0 OP2 A:G733 3.8 66.3 1.0 C6 A:A761 3.9 64.4 1.0 N9 A:G733 4.2 66.3 1.0 OP2 A:A761 4.2 64.4 1.0 C4 A:G733 4.3 66.3 1.0 N9 A:A761 4.3 64.4 1.0 C4 A:A761 4.4 64.4 1.0 OP2 A:C732 4.5 67.4 1.0 OP2 A:G760 4.5 65.0 1.0 C5 A:C732 4.7 67.4 1.0 O5' A:G733 4.7 66.3 1.0 C6 A:C732 4.9 67.4 1.0 P A:G733 4.9 66.3 1.0

E.B.Pichkur, A.Paleskava, A.G.Tereshchenkov, P.Kasatsky, E.S.Komarova, D.I.Shiriaev, A.A.Bogdanov, O.A.Dontsova, I.A.Osterman, P.V.Sergiev, Y.S.Polikanov, A.G.Myasnikov, A.L.Konevega. Insights Into the Improved Macrolide Inhibitory Activity From the High-Resolution Cryo-Em Structure of Dirithromycin Bound to Thee. COLI70S Ribosome. Rna V. 26 715 2020.
ISSN: ESSN 1469-9001
PubMed: 32144191
DOI: 10.1261/RNA.073817.119