Magnesium in PDB 2otj: 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj was solved by G.Blaha, S.J.Schroeder, J.Tirado-Rives, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.70 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.738, 299.519, 573.593, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.8

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 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 - 117;

Binding sites:

The binding sites of Magnesium atom in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui (pdb code 2otj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:44.4 occ:1.00 O 0:HOH7774 1.9 25.9 1.0 OP2 0:C2534 1.9 45.4 1.0 O 0:HOH9179 2.0 53.0 1.0 OP2 0:C2533 2.0 45.1 1.0 O 0:HOH3633 2.1 35.5 1.0 OP2 0:A2483 2.3 44.3 1.0 O3' 0:G2482 3.2 44.5 1.0 P 0:A2483 3.3 43.8 1.0 P 0:C2534 3.4 45.2 1.0 P 0:C2533 3.4 47.0 1.0 O2' 0:A2532 3.9 47.2 1.0 O3' 0:A2532 3.9 46.7 1.0 O 0:HOH9649 4.0 59.1 1.0 O3' 0:C2533 4.2 43.5 1.0 OP1 0:A2483 4.2 44.4 1.0 O 0:HOH4358 4.2 36.2 1.0 OP2 0:U2484 4.2 44.8 1.0 OP1 0:C2534 4.2 45.0 1.0 O2' 0:G2482 4.3 43.3 1.0 O5' 0:C2534 4.3 44.7 1.0 C3' 0:C2533 4.4 43.0 1.0 O5' 0:C2533 4.4 44.8 1.0 OP1 0:C2533 4.5 47.2 1.0 O5' 0:A2483 4.5 43.8 1.0 O 0:HOH6395 4.6 59.0 1.0 C3' 0:G2482 4.6 43.9 1.0 C5' 0:A2483 4.8 42.3 1.0 C5 0:C2534 4.8 48.5 1.0 O 0:HOH7483 4.8 48.5 1.0 C2' 0:G2482 4.9 43.9 1.0 C3' 0:A2532 4.9 47.2 1.0 C2' 0:A2532 4.9 47.0 1.0

Magnesium binding site 2 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:40.2 occ:1.00 OP1 0:A2483 2.0 44.4 1.0 O 0:HOH4358 2.0 36.2 1.0 O 0:HOH7752 2.0 39.2 1.0 O6 0:G627 2.0 38.4 1.0 O 0:HOH7753 2.2 23.7 1.0 OP1 0:C2534 2.3 45.0 1.0 P 0:A2483 3.2 43.8 1.0 C6 0:G627 3.3 37.9 1.0 O 0:HOH9265 3.5 21.5 1.0 P 0:C2534 3.6 45.2 1.0 O 0:HOH7121 3.6 63.0 1.0 OP2 0:A2483 3.7 44.3 1.0 O4 0:U626 3.8 38.2 1.0 N1 0:G627 4.0 38.1 1.0 O 0:HOH5908 4.0 50.8 1.0 OP2 0:C2534 4.1 45.4 1.0 O5' 0:A2483 4.1 43.8 1.0 O 0:HOH3545 4.2 49.4 1.0 O2' 0:U625 4.2 38.0 1.0 C5 0:U626 4.3 38.8 1.0 O3' 0:C2533 4.3 43.5 1.0 C4 0:U626 4.3 39.0 1.0 O3' 0:G2482 4.4 44.5 1.0 C5 0:G627 4.4 37.4 1.0 OP2 0:U2535 4.4 47.7 1.0 O5' 0:C2534 4.7 44.7 1.0 N7 0:G627 4.8 36.7 1.0 C3' 0:G2482 4.9 43.9 1.0

Magnesium binding site 3 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:36.1 occ:1.00 O 0:HOH9838 1.9 45.0 1.0 O 0:HOH3684 2.0 51.2 1.0 OP2 0:G877 2.1 31.9 1.0 OP2 0:A876 2.1 33.4 1.0 OP1 0:A2624 2.1 32.8 1.0 O A:HOH8811 2.3 30.8 1.0 P 0:G877 3.4 31.6 1.0 P 0:A876 3.4 33.5 1.0 P 0:A2624 3.5 32.5 1.0 O3' 0:A875 3.9 32.4 1.0 O 0:HOH6301 3.9 48.8 1.0 OP1 0:G877 4.0 32.3 1.0 O5' 0:A876 4.0 32.2 1.0 OD1 A:ASN195 4.1 36.6 1.0 O3' 0:G2623 4.1 33.2 1.0 O3' 0:A876 4.1 30.9 1.0 O A:ALA193 4.2 36.4 1.0 O 0:HOH9020 4.3 40.0 1.0 C5' 0:A876 4.4 32.9 1.0 O A:HOH8839 4.4 35.9 1.0 OP2 0:A2624 4.4 33.9 1.0 O A:HOH8912 4.5 64.5 1.0 O5' 0:G877 4.5 30.9 1.0 O5' 0:A2624 4.5 33.6 1.0 C3' 0:A876 4.6 32.8 1.0 O A:HOH8861 4.6 28.7 1.0 OP1 0:A876 4.6 32.6 1.0 C5' 0:A2624 4.7 36.2 1.0 CG A:ASN195 4.9 35.3 1.0

Magnesium binding site 4 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:37.4 occ:1.00 O 0:HOH9788 1.9 45.7 1.0 O 0:HOH9047 1.9 38.6 1.0 OP1 0:A459 2.0 35.4 1.0 O6 0:G456 2.0 39.0 1.0 O 0:HOH7759 2.1 28.4 1.0 O 0:HOH3804 2.2 27.2 1.0 C6 0:G456 3.2 39.6 1.0 P 0:A459 3.3 36.1 1.0 O5' 0:A459 3.8 35.3 1.0 O 0:HOH3721 3.9 43.3 1.0 C5 0:G456 4.0 39.0 1.0 C5' 0:A459 4.0 35.6 1.0 N7 0:G456 4.1 38.8 1.0 O 0:HOH3531 4.2 24.6 1.0 OP2 0:A459 4.2 37.3 1.0 N1 0:G456 4.3 39.8 1.0 O 0:HOH9338 4.3 48.9 1.0 CE C:LYS85 4.4 30.2 1.0 O3' 0:G458 4.4 35.7 1.0 OP1 0:A460 4.4 37.8 1.0 OP2 0:A455 4.5 36.0 1.0 N7 0:A455 4.5 43.0 1.0 OP1 0:A477 4.6 33.0 1.0 O 0:HOH5991 4.6 53.0 1.0 CD C:LYS85 4.7 30.3 1.0 NZ C:LYS85 4.7 29.4 1.0 O 0:HOH5433 4.9 62.6 1.0

Magnesium binding site 5 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:32.2 occ:1.00 O 0:HOH7775 1.9 32.8 1.0 OP2 0:A1839 1.9 35.8 1.0 O 0:HOH7776 1.9 35.2 1.0 OP1 0:U1838 2.0 35.6 1.0 OP1 0:A1836 2.2 34.5 1.0 O 0:HOH3630 2.4 32.0 1.0 P 0:A1839 3.4 35.4 1.0 P 0:U1838 3.4 35.7 1.0 P 0:A1836 3.6 34.3 1.0 O 0:HOH5591 3.9 54.8 1.0 O 0:HOH5533 4.0 57.0 1.0 O5' 0:U1838 4.2 35.6 1.0 OP1 0:A1839 4.2 35.8 1.0 O 0:HOH9006 4.2 35.3 1.0 O5' 0:A1836 4.2 35.8 1.0 OP2 0:A1836 4.2 34.6 1.0 C3' 0:G1837 4.2 34.0 1.0 O5' 0:A1839 4.2 34.2 1.0 O3' 0:U1838 4.3 35.4 1.0 OP2 0:U1838 4.3 34.8 1.0 C5' 0:U1838 4.3 33.8 1.0 O3' 0:G1837 4.3 33.6 1.0 O 0:HOH9646 4.4 70.4 1.0 O 0:HOH7849 4.4 37.9 1.0 OP2 0:G1837 4.4 33.1 1.0 C3' 0:U1838 4.5 34.5 1.0 C2' 0:U1835 4.6 35.6 1.0 O3' 0:U1835 4.7 33.6 1.0 N7 0:A1839 4.7 34.8 1.0 O 0:HOH9525 4.8 50.9 1.0 C3' 0:U1835 4.8 34.5 1.0 C8 0:A1839 4.8 34.8 1.0

Magnesium binding site 6 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:36.5 occ:1.00 O 0:HOH3635 1.9 51.3 1.0 OP2 0:C822 1.9 47.4 1.0 OP1 0:G854 2.0 38.7 1.0 O 0:HOH9820 2.1 35.7 1.0 OP2 0:U821 2.1 42.7 1.0 O 0:HOH3773 2.6 67.8 1.0 P 0:G854 3.2 38.6 1.0 P 0:C822 3.3 46.8 1.0 P 0:U821 3.6 40.5 1.0 O 0:HOH3221 3.7 70.0 1.0 OP2 0:G854 3.8 39.6 1.0 OP1 0:U855 3.8 40.7 1.0 O5' 0:G854 3.9 36.7 1.0 NA 0:NA8527 3.9 62.0 1.0 O5' 0:U821 4.0 43.1 1.0 OP1 0:G856 4.0 44.7 1.0 OP1 0:C822 4.1 45.5 1.0 O3' 0:U821 4.1 44.3 1.0 C5' 0:G854 4.1 36.2 1.0 C3' 0:U821 4.2 43.1 1.0 O3' 0:G820 4.3 41.0 1.0 O5' 0:C822 4.3 46.8 1.0 O 0:HOH5024 4.4 76.6 1.0 O3' 0:C853 4.4 38.2 1.0 OP1 0:U821 4.6 40.3 1.0 C5 0:C822 4.9 49.5 1.0 O 0:HOH9037 5.0 63.2 1.0

Magnesium binding site 7 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:26.6 occ:1.00 O 0:HOH7764 1.8 20.2 1.0 OP2 0:U832 1.9 36.7 1.0 O 0:HOH9006 1.9 35.3 1.0 OP2 0:A1840 2.2 34.9 1.0 OP1 0:A1839 2.2 35.8 1.0 O 0:HOH3372 2.3 29.4 1.0 P 0:U832 3.3 36.8 1.0 O 0:HOH9101 3.3 75.2 1.0 P 0:A1840 3.3 35.3 1.0 OP1 0:A1840 3.6 35.9 1.0 P 0:A1839 3.7 35.4 1.0 O 0:HOH9646 3.7 70.4 1.0 OP1 0:U832 3.9 36.1 1.0 O5' 0:U832 4.2 36.5 1.0 O 0:HOH6373 4.2 60.3 1.0 O3' 0:U831 4.3 37.5 1.0 OP2 0:A1839 4.4 35.8 1.0 O3' 0:A1839 4.4 34.8 1.0 O5' 0:A1840 4.4 35.3 1.0 O5' 0:A1839 4.5 34.2 1.0 O3' 0:U1838 4.6 35.4 1.0 C3' 0:U831 4.7 37.8 1.0 O 0:HOH7775 4.7 32.8 1.0 C5' 0:U832 4.8 37.3 1.0 C3' 0:A1839 4.8 34.6 1.0 C5' 0:A1839 4.8 34.2 1.0 O 0:HOH7849 4.9 37.9 1.0 OP2 0:G833 4.9 36.5 1.0 O 0:HOH9975 4.9 45.8 1.0

Magnesium binding site 8 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:29.1 occ:1.00 OP1 0:A2465 1.9 39.6 1.0 OP1 0:U919 1.9 33.0 1.0 O 0:HOH7768 2.1 30.4 1.0 OP1 0:C2464 2.4 36.5 1.0 O 0:HOH7850 2.4 49.5 1.0 O 0:HOH3648 2.5 22.7 1.0 P 0:U919 3.1 33.3 1.0 P 0:A2465 3.1 40.0 1.0 O5' 0:A2465 3.5 38.6 1.0 OP2 0:U919 3.5 33.8 1.0 O 0:HOH9558 3.6 39.7 1.0 P 0:C2464 3.6 37.0 1.0 O5' 0:U919 3.9 32.2 1.0 OP2 0:A2465 3.9 41.8 1.0 O5' 0:C2464 4.1 37.7 1.0 C5' 0:C2464 4.1 38.9 1.0 OP2 0:C2464 4.3 37.8 1.0 O 0:HOH9459 4.3 48.2 1.0 O 0:HOH5920 4.3 55.3 1.0 O3' 0:G918 4.3 32.5 1.0 C5' 0:U919 4.4 33.3 1.0 O3' 0:C2464 4.4 40.0 1.0 C5' 0:A2465 4.5 37.0 1.0 C3' 0:A2465 4.5 38.0 1.0 O 0:HOH3364 4.6 36.8 1.0 OP1 0:G2466 4.7 39.5 1.0 C3' 0:C2464 4.8 39.6 1.0 C2' 0:A2465 4.8 37.6 1.0 O3' 0:A2463 4.8 38.2 1.0 O 0:HOH9935 4.9 51.6 1.0 OP1 0:G2293 4.9 43.4 1.0

Magnesium binding site 9 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:36.3 occ:1.00 O 0:HOH7770 1.9 38.1 1.0 OP1 0:A2612 1.9 30.7 1.0 OP1 0:G2611 2.1 37.0 1.0 O 0:HOH7769 2.1 32.3 1.0 O 0:HOH3758 2.1 48.7 1.0 O 0:HOH7440 2.2 39.7 1.0 P 0:G2611 3.2 36.9 1.0 O3' 0:U2610 3.3 36.2 1.0 P 0:A2612 3.4 32.2 1.0 OP2 0:G2093 3.7 33.8 1.0 C5' 0:G2611 3.9 34.7 1.0 O 0:HOH9339 3.9 35.3 1.0 O5' 0:G2611 4.0 35.6 1.0 O 0:HOH9479 4.1 44.0 1.0 OP2 0:G2094 4.1 32.1 1.0 O3' 0:G2611 4.1 33.2 1.0 O5' 0:A2612 4.3 33.6 1.0 OP2 0:A2612 4.3 32.9 1.0 OP1 0:G2094 4.3 32.1 1.0 NA 0:NA8558 4.4 75.3 1.0 C3' 0:G2611 4.4 33.3 1.0 OP2 0:G2611 4.5 34.6 1.0 O 0:HOH9311 4.5 30.7 1.0 C3' 0:U2610 4.6 36.4 1.0 P 0:G2094 4.7 33.6 1.0 C4' 0:G2611 4.7 33.9 1.0 O2' 0:U2610 4.9 35.6 1.0 C4' 0:U2610 4.9 36.4 1.0

Magnesium binding site 10 out of 117 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:11.2 occ:1.00 O 0:HOH9277 1.6 36.8 1.0 O 0:HOH3862 1.7 42.9 1.0 O 0:HOH9369 1.9 40.3 1.0 OP1 0:G836 2.0 36.2 1.0 OP1 0:U2615 2.2 36.4 1.0 OE1 B:GLN230 2.4 34.8 1.0 P 0:G836 3.4 38.3 1.0 CD B:GLN230 3.5 34.6 1.0 P 0:U2615 3.6 37.1 1.0 O 0:HOH5068 3.8 31.8 1.0 CG B:GLN230 4.0 35.5 1.0 CB B:GLN230 4.0 35.7 1.0 O 0:HOH9211 4.1 31.9 1.0 O 0:HOH9560 4.2 64.8 1.0 C5' 0:G836 4.2 34.8 1.0 OP2 0:G836 4.2 38.3 1.0 O5' 0:G836 4.2 36.0 1.0 O3' 0:U835 4.4 36.2 1.0 C3' 0:U835 4.4 37.7 1.0 O 0:HOH4020 4.4 54.4 1.0 O 0:HOH6843 4.4 55.1 1.0 OP2 0:U2615 4.4 35.7 1.0 O5' 0:U2615 4.5 36.8 1.0 O3' 0:C2614 4.5 35.9 1.0 CA B:GLN230 4.6 35.2 1.0 OP2 0:G2616 4.6 36.4 1.0 NE2 B:GLN230 4.6 34.0 1.0 O B:GLN230 4.7 36.2 1.0 C5' 0:U835 4.8 36.5 1.0 N2 0:G2616 4.9 36.4 1.0

S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, P.B.Moore. The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula Marismortui: 13-Deoxytedanolide and Girodazole. J.Mol.Biol. V. 367 1471 2007.
ISSN: ISSN 0022-2836
PubMed: 17321546
DOI: 10.1016/J.JMB.2007.01.081