Magnesium in PDB 1kd1: Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1 was solved by J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 26.9

The structure of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	85 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 - 119;

Binding sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1kd1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 119 binding sites of Magnesium where determined in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8001 b:39.4 occ:1.00 O A:HOH7774 1.9 20.0 1.0 O A:HOH9173 2.0 47.6 1.0 O A:HOH3611 2.0 29.7 1.0 OP2 A:C2533 2.1 29.8 1.0 OP2 A:C2534 2.1 35.8 1.0 OP2 A:A2483 2.5 36.2 1.0 P A:C2533 3.5 31.6 1.0 O3' A:G2482 3.5 37.1 1.0 P A:A2483 3.5 36.4 1.0 P A:C2534 3.6 35.8 1.0 O A:HOH9632 3.8 38.0 1.0 O3' A:A2532 3.9 33.6 1.0 O2' A:A2532 4.0 35.7 1.0 O A:HOH4319 4.2 50.6 1.0 O A:HOH6369 4.2 61.8 1.0 OP2 A:U2484 4.2 42.7 1.0 O2' A:G2482 4.3 39.2 1.0 O3' A:C2533 4.4 35.0 1.0 O5' A:C2533 4.4 31.5 1.0 OP1 A:A2483 4.4 37.1 1.0 OP1 A:C2533 4.4 34.4 1.0 OP1 A:C2534 4.4 34.7 1.0 O5' A:C2534 4.5 36.2 1.0 C3' A:C2533 4.5 34.3 1.0 C5 A:C2534 4.6 42.0 1.0 O5' A:A2483 4.7 36.2 1.0 O A:HOH7480 4.8 39.0 1.0 C3' A:G2482 4.8 38.2 1.0 MG A:MG8002 4.9 31.7 1.0 C5' A:A2483 4.9 36.6 1.0 C3' A:A2532 4.9 35.0 1.0 C2' A:A2532 5.0 35.9 1.0 OP2 A:A2485 5.0 41.7 1.0

Magnesium binding site 2 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8002 b:31.7 occ:1.00 OP1 A:A2483 1.9 37.1 1.0 OP1 A:C2534 2.0 34.7 1.0 O A:HOH7753 2.0 26.7 1.0 O6 A:G627 2.1 31.1 1.0 O A:HOH4319 2.2 50.6 1.0 O A:HOH7752 2.3 17.0 1.0 P A:A2483 3.0 36.4 1.0 P A:C2534 3.2 35.8 1.0 C6 A:G627 3.3 30.6 1.0 OP2 A:A2483 3.3 36.2 1.0 OP2 A:C2534 3.7 35.8 1.0 O4 A:U626 3.9 36.2 1.0 N1 A:G627 3.9 30.6 1.0 O5' A:A2483 4.0 36.2 1.0 O3' A:C2533 4.1 35.0 1.0 O A:HOH9255 4.1 14.1 1.0 O A:HOH5869 4.1 62.9 1.0 O3' A:G2482 4.1 37.1 1.0 OP2 A:U2535 4.2 42.3 1.0 O A:HOH7097 4.4 44.1 1.0 O5' A:C2534 4.4 36.2 1.0 C5 A:G627 4.5 30.7 1.0 O2' A:U625 4.5 33.5 1.0 C4 A:U626 4.6 35.0 1.0 C5 A:U626 4.6 34.0 1.0 C3' A:G2482 4.6 38.2 1.0 O A:HOH3526 4.7 61.4 1.0 C5' A:C2534 4.9 38.3 1.0 MG A:MG8001 4.9 39.4 1.0 OP2 A:C2533 5.0 29.8 1.0

Magnesium binding site 3 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8003 b:24.6 occ:1.00 OP1 A:A2624 1.9 31.4 1.0 OP2 A:G877 1.9 32.7 1.0 O C:HOH8511 2.2 31.8 1.0 OP2 A:A876 2.2 32.9 1.0 O C:HOH8536 2.4 36.0 1.0 O A:HOH3662 2.5 35.2 1.0 P A:G877 3.1 33.7 1.0 P A:A2624 3.3 33.2 1.0 OP1 A:G877 3.5 33.3 1.0 P A:A876 3.6 33.9 1.0 O3' A:G2623 3.7 32.2 1.0 O3' A:A876 4.0 31.8 1.0 O A:HOH9021 4.0 39.6 1.0 O A:HOH6269 4.0 37.7 1.0 OD1 C:ASN195 4.0 36.6 1.0 O3' A:A875 4.1 32.1 1.0 O5' A:A876 4.1 33.7 1.0 OP2 A:A2624 4.2 34.2 1.0 O A:HOH7160 4.2 62.1 1.0 C5' A:A876 4.3 33.1 1.0 O5' A:G877 4.3 32.0 1.0 O5' A:A2624 4.3 34.0 1.0 O C:ALA193 4.4 34.1 1.0 C3' A:A876 4.5 32.7 1.0 O C:HOH8625 4.6 34.8 1.0 C5' A:A2624 4.6 33.4 1.0 O A:HOH4467 4.7 38.1 1.0 O A:HOH7783 4.8 28.5 1.0 OP1 A:A876 4.8 34.3 1.0 CG C:ASN195 4.9 33.9 1.0 C4' A:A876 4.9 32.8 1.0 O C:HOH8548 5.0 81.0 1.0

Magnesium binding site 4 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8004 b:48.5 occ:1.00 OP1 A:A459 1.6 28.8 1.0 O A:HOH9770 1.7 29.9 1.0 O A:HOH9045 1.8 23.8 1.0 O A:HOH3778 2.1 22.3 1.0 O6 A:G456 2.1 41.5 1.0 O A:HOH7759 2.3 23.1 1.0 P A:A459 3.0 30.9 1.0 C6 A:G456 3.3 41.0 1.0 O5' A:A459 3.6 31.3 1.0 C5' A:A459 3.9 31.6 1.0 OP2 A:A459 3.9 32.8 1.0 O A:HOH9330 4.0 55.1 1.0 O3' A:G458 4.0 32.4 1.0 C5 A:G456 4.1 39.6 1.0 N7 A:G456 4.1 38.0 1.0 O A:HOH3698 4.2 62.3 1.0 CE E:LYS85 4.3 31.5 1.0 OP1 A:A460 4.3 38.0 1.0 O A:HOH5952 4.3 45.2 1.0 N1 A:G456 4.4 42.1 1.0 NZ E:LYS85 4.5 32.1 1.0 O A:HOH3512 4.5 35.0 1.0 OP2 A:A455 4.6 29.3 1.0 OP1 A:A477 4.6 36.1 1.0 OP2 A:A477 4.7 34.5 1.0 CD E:LYS85 4.8 32.6 1.0 O A:HOH5399 4.8 23.6 1.0 N7 A:A455 4.9 40.5 1.0

Magnesium binding site 5 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8005 b:44.0 occ:1.00 O A:HOH7776 1.7 41.7 1.0 O A:HOH7775 1.8 24.8 1.0 OP2 A:A1839 1.9 26.7 1.0 OP1 A:A1836 2.1 29.9 1.0 OP1 A:U1838 2.1 33.6 1.0 O A:HOH3607 2.5 25.5 1.0 P A:A1839 3.3 28.2 1.0 P A:U1838 3.5 31.1 1.0 P A:A1836 3.5 29.7 1.0 O A:HOH5554 3.7 64.8 1.0 O A:HOH9008 3.9 23.3 1.0 O A:HOH5495 4.0 37.4 1.0 O A:HOH7853 4.1 60.0 1.0 O5' A:A1839 4.1 29.8 1.0 O3' A:U1838 4.2 28.9 1.0 OP1 A:A1839 4.2 28.5 1.0 OP2 A:U1838 4.2 31.9 1.0 O5' A:A1836 4.2 33.2 1.0 O5' A:U1838 4.3 29.9 1.0 O A:HOH9629 4.3 49.2 1.0 C3' A:G1837 4.4 38.6 1.0 O3' A:U1835 4.4 30.2 1.0 OP2 A:A1836 4.4 31.6 1.0 C2' A:U1835 4.5 36.4 1.0 OP2 A:G1837 4.5 39.5 1.0 O3' A:G1837 4.5 34.0 1.0 C3' A:U1838 4.5 28.6 1.0 C3' A:U1835 4.5 34.1 1.0 C5' A:U1838 4.6 28.9 1.0 O A:HOH9505 4.7 26.5 1.0 N7 A:A1839 4.8 34.4 1.0 C8 A:A1839 4.8 34.3 1.0 O2' A:U1835 5.0 39.5 1.0

Magnesium binding site 6 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8006 b:48.1 occ:1.00 OP2 A:C822 1.7 48.2 1.0 O A:HOH9805 2.0 41.7 1.0 OP2 A:U821 2.1 43.9 1.0 OP1 A:G854 2.2 34.5 1.0 O A:HOH3750 2.2 36.6 1.0 O A:HOH3613 2.3 31.4 1.0 P A:C822 3.0 49.7 1.0 P A:U821 3.4 44.1 1.0 P A:G854 3.4 34.3 1.0 O3' A:U821 3.7 49.5 1.0 O5' A:U821 3.7 46.6 1.0 C3' A:U821 3.8 48.5 1.0 OP1 A:C822 3.8 47.4 1.0 O A:HOH3203 3.8 52.6 1.0 OP1 A:G856 3.9 43.1 1.0 OP2 A:G854 4.0 33.3 1.0 NA A:NA8327 4.1 33.0 1.0 O5' A:C822 4.1 49.9 1.0 O5' A:G854 4.1 32.7 1.0 O3' A:G820 4.3 43.0 1.0 C5' A:G854 4.4 34.9 1.0 O A:HOH4997 4.5 36.4 1.0 OP1 A:U821 4.5 43.5 1.0 OP1 A:U855 4.5 38.7 1.0 O3' A:C853 4.6 33.8 1.0 O A:HOH9304 4.8 0.8 1.0 C2' A:U821 4.8 47.9 1.0 C4' A:U821 4.8 49.4 1.0 C5' A:U821 4.8 48.7 1.0 C5 A:C822 4.8 49.2 1.0 O A:HOH9722 4.8 62.3 1.0

Magnesium binding site 7 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8007 b:23.7 occ:1.00 O A:HOH7764 1.6 13.1 1.0 OP2 A:U832 1.9 37.9 1.0 OP2 A:A1840 2.1 29.0 1.0 OP1 A:A1839 2.2 28.5 1.0 O A:HOH9008 2.2 23.3 1.0 O A:HOH3357 2.4 28.4 1.0 P A:A1840 3.3 29.7 1.0 P A:U832 3.3 36.3 1.0 P A:A1839 3.6 28.2 1.0 OP1 A:A1840 3.7 27.6 1.0 O A:HOH9629 3.8 49.2 1.0 O A:HOH9101 3.8 41.2 1.0 O A:HOH6346 3.9 42.1 1.0 OP1 A:U832 3.9 35.2 1.0 O5' A:U832 4.1 36.2 1.0 O3' A:A1839 4.2 29.5 1.0 OP2 A:A1839 4.2 26.7 1.0 O3' A:U831 4.3 35.9 1.0 O5' A:A1840 4.4 29.5 1.0 O5' A:A1839 4.5 29.8 1.0 O3' A:U1838 4.5 28.9 1.0 C5' A:U832 4.5 36.8 1.0 O A:HOH7883 4.6 42.0 1.0 C3' A:A1839 4.6 31.7 1.0 OP2 A:G833 4.7 39.9 1.0 C5' A:A1839 4.7 30.6 1.0 C3' A:U831 4.8 36.5 1.0 O A:HOH7853 4.9 60.0 1.0

Magnesium binding site 8 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8008 b:49.3 occ:1.00 OP1 A:U919 1.7 33.6 1.0 O A:HOH7768 1.9 23.4 1.0 OP1 A:A2465 2.2 49.1 1.0 O A:HOH7854 2.3 39.9 1.0 OP1 A:C2464 2.3 42.6 1.0 O A:HOH3625 2.7 35.5 1.0 P A:U919 2.9 32.7 1.0 O5' A:U919 3.4 32.5 1.0 P A:A2465 3.5 48.3 1.0 OP2 A:U919 3.6 33.1 1.0 P A:C2464 3.7 43.3 1.0 O5' A:A2465 3.8 48.0 1.0 C5' A:U919 3.8 33.7 1.0 O A:HOH5879 3.9 96.1 1.0 OP1 A:G2466 3.9 54.5 1.0 O A:HOH3347 4.0 81.1 1.0 O A:HOH9442 4.0 61.5 1.0 O3' A:G918 4.1 33.7 1.0 C5' A:C2464 4.2 48.0 1.0 O5' A:C2464 4.2 45.1 1.0 O A:HOH9539 4.2 44.7 1.0 OP2 A:A2465 4.3 47.3 1.0 O A:HOH9912 4.3 71.8 1.0 C3' A:A2465 4.3 49.9 1.0 C2' A:A2465 4.6 49.2 1.0 OP2 A:C2464 4.7 43.6 1.0 C5' A:A2465 4.7 47.3 1.0 O3' A:A2463 4.7 43.1 1.0 O3' A:C2464 4.7 48.4 1.0 C5' A:G2466 4.9 52.5 1.0

Magnesium binding site 9 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8009 b:20.3 occ:1.00 O A:HOH7770 1.5 62.5 1.0 O A:HOH7429 1.8 45.9 1.0 OP1 A:A2612 1.8 29.3 1.0 OP1 A:G2611 2.1 29.4 1.0 O A:HOH7769 2.3 20.1 1.0 O A:HOH3736 2.4 24.4 1.0 P A:A2612 3.1 29.4 1.0 P A:G2611 3.4 29.6 1.0 O A:HOH9331 3.4 43.2 1.0 O3' A:U2610 3.6 30.1 1.0 OP2 A:A2612 3.6 30.3 1.0 O A:HOH7771 3.7 53.9 1.0 OP2 A:G2093 3.9 32.4 1.0 O A:HOH9301 4.0 55.7 1.0 C5' A:G2611 4.1 30.5 1.0 O3' A:G2611 4.1 31.7 1.0 O5' A:A2612 4.1 33.3 1.0 O5' A:G2611 4.1 29.3 1.0 OP1 A:G2094 4.2 25.9 1.0 OP2 A:G2094 4.2 25.7 1.0 C3' A:G2611 4.4 32.8 1.0 O A:HOH9462 4.4 36.2 1.0 OP2 A:G2611 4.6 30.8 1.0 P A:G2094 4.7 25.9 1.0 O A:HOH7786 4.8 50.7 1.0 C4' A:G2611 4.8 31.2 1.0 C3' A:U2610 4.9 31.4 1.0 O A:HOH3188 5.0 49.1 1.0

Magnesium binding site 10 out of 119 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8010 b:40.5 occ:1.00 OP1 A:G836 1.4 30.1 1.0 O D:HOH8526 1.8 32.1 1.0 O A:HOH3834 1.9 24.2 1.0 O A:HOH9356 2.2 29.0 1.0 OE1 D:GLN230 2.2 35.3 1.0 OP1 A:U2615 2.6 34.2 1.0 P A:G836 2.8 28.6 1.0 CD D:GLN230 3.4 33.5 1.0 C5' A:G836 3.6 30.7 1.0 O5' A:G836 3.6 29.2 1.0 OP2 A:G836 3.7 29.6 1.0 O3' A:U835 3.8 29.2 1.0 C3' A:U835 4.0 30.2 1.0 P A:U2615 4.0 35.8 1.0 O A:HOH5041 4.0 60.5 1.0 O A:HOH3984 4.2 49.2 1.0 CG D:GLN230 4.2 32.5 1.0 CB D:GLN230 4.3 31.6 1.0 NE2 D:GLN230 4.4 32.3 1.0 O A:HOH6816 4.4 39.5 1.0 C5' A:U835 4.5 33.4 1.0 O A:HOH9201 4.6 31.0 1.0 OP2 A:U2615 4.6 36.9 1.0 CA D:GLN230 4.7 32.8 1.0 O A:HOH9541 4.8 25.5 1.0 O D:GLN230 4.8 33.8 1.0 C4' A:U835 4.8 31.5 1.0 OP2 A:G2616 4.9 33.0 1.0 O3' A:C2614 4.9 34.7 1.0 O5' A:U2615 5.0 35.4 1.0 O A:HOH9060 5.0 22.4 1.0

J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz. The Structures of Four Macrolide Antibiotics Bound to the Large Ribosomal Subunit. Mol.Cell V. 10 117 2002.
ISSN: ISSN 1097-2765
PubMed: 12150912
DOI: 10.1016/S1097-2765(02)00570-1